Modelling infant mortality rate in Central Java, Indonesia use generalized poisson regression method

NASA Astrophysics Data System (ADS)

Prahutama, Alan; Sudarno

2018-05-01

The infant mortality rate is the number of deaths under one year of age occurring among the live births in a given geographical area during a given year, per 1,000 live births occurring among the population of the given geographical area during the same year. This problem needs to be addressed because it is an important element of a country’s economic development. High infant mortality rate will disrupt the stability of a country as it relates to the sustainability of the population in the country. One of regression model that can be used to analyze the relationship between dependent variable Y in the form of discrete data and independent variable X is Poisson regression model. Recently The regression modeling used for data with dependent variable is discrete, among others, poisson regression, negative binomial regression and generalized poisson regression. In this research, generalized poisson regression modeling gives better AIC value than poisson regression. The most significant variable is the Number of health facilities (X1), while the variable that gives the most influence to infant mortality rate is the average breastfeeding (X9).

Computation of solar perturbations with Poisson series

NASA Technical Reports Server (NTRS)

Broucke, R.

1974-01-01

Description of a project for computing first-order perturbations of natural or artificial satellites by integrating the equations of motion on a computer with automatic Poisson series expansions. A basic feature of the method of solution is that the classical variation-of-parameters formulation is used rather than rectangular coordinates. However, the variation-of-parameters formulation uses the three rectangular components of the disturbing force rather than the classical disturbing function, so that there is no problem in expanding the disturbing function in series. Another characteristic of the variation-of-parameters formulation employed is that six rather unusual variables are used in order to avoid singularities at the zero eccentricity and zero (or 90 deg) inclination. The integration process starts by assuming that all the orbit elements present on the right-hand sides of the equations of motion are constants. These right-hand sides are then simple Poisson series which can be obtained with the use of the Bessel expansions of the two-body problem in conjunction with certain interation methods. These Poisson series can then be integrated term by term, and a first-order solution is obtained.

A coarse-grid-projection acceleration method for finite-element incompressible flow computations

NASA Astrophysics Data System (ADS)

Kashefi, Ali; Staples, Anne; FiN Lab Team

2015-11-01

Coarse grid projection (CGP) methodology provides a framework for accelerating computations by performing some part of the computation on a coarsened grid. We apply the CGP to pressure projection methods for finite element-based incompressible flow simulations. Based on it, the predicted velocity field data is restricted to a coarsened grid, the pressure is determined by solving the Poisson equation on the coarse grid, and the resulting data are prolonged to the preset fine grid. The contributions of the CGP method to the pressure correction technique are twofold: first, it substantially lessens the computational cost devoted to the Poisson equation, which is the most time-consuming part of the simulation process. Second, it preserves the accuracy of the velocity field. The velocity and pressure spaces are approximated by Galerkin spectral element using piecewise linear basis functions. A restriction operator is designed so that fine data are directly injected into the coarse grid. The Laplacian and divergence matrices are driven by taking inner products of coarse grid shape functions. Linear interpolation is implemented to construct a prolongation operator. A study of the data accuracy and the CPU time for the CGP-based versus non-CGP computations is presented. Laboratory for Fluid Dynamics in Nature.

Normalized stiffness ratios for mechanical characterization of isotropic acoustic foams.

PubMed

Sahraoui, Sohbi; Brouard, Bruno; Benyahia, Lazhar; Parmentier, Damien; Geslain, Alan

2013-12-01

This paper presents a method for the mechanical characterization of isotropic foams at low frequency. The objective of this study is to determine the Young's modulus, the Poisson's ratio, and the loss factor of commercially available foam plates. The method is applied on porous samples having square and circular sections. The main idea of this work is to perform quasi-static compression tests of a single foam sample followed by two juxtaposed samples having the same dimensions. The load and displacement measurements lead to a direct extraction of the elastic constants by means of normalized stiffness and normalized stiffness ratio which depend on Poisson's ratio and shape factor. The normalized stiffness is calculated by the finite element method for different Poisson ratios. The no-slip boundary conditions imposed by the loading rigid plates create interfaces with a complex strain distribution. Beforehand, compression tests were performed by means of a standard tensile machine in order to determine the appropriate pre-compression rate for quasi-static tests.

Effects of adaptive refinement on the inverse EEG solution

NASA Astrophysics Data System (ADS)

Weinstein, David M.; Johnson, Christopher R.; Schmidt, John A.

1995-10-01

One of the fundamental problems in electroencephalography can be characterized by an inverse problem. Given a subset of electrostatic potentials measured on the surface of the scalp and the geometry and conductivity properties within the head, calculate the current vectors and potential fields within the cerebrum. Mathematically the generalized EEG problem can be stated as solving Poisson's equation of electrical conduction for the primary current sources. The resulting problem is mathematically ill-posed i.e., the solution does not depend continuously on the data, such that small errors in the measurement of the voltages on the scalp can yield unbounded errors in the solution, and, for the general treatment of a solution of Poisson's equation, the solution is non-unique. However, if accurate solutions the general treatment of a solution of Poisson's equation, the solution is non-unique. However, if accurate solutions to such problems could be obtained, neurologists would gain noninvasive accesss to patient-specific cortical activity. Access to such data would ultimately increase the number of patients who could be effectively treated for pathological cortical conditions such as temporal lobe epilepsy. In this paper, we present the effects of spatial adaptive refinement on the inverse EEG problem and show that the use of adaptive methods allow for significantly better estimates of electric and potential fileds within the brain through an inverse procedure. To test these methods, we have constructed several finite element head models from magneteic resonance images of a patient. The finite element meshes ranged in size from 2724 nodes and 12,812 elements to 5224 nodes and 29,135 tetrahedral elements, depending on the level of discretization. We show that an adaptive meshing algorithm minimizes the error in the forward problem due to spatial discretization and thus increases the accuracy of the inverse solution.

Stabilized finite element methods to simulate the conductances of ion channels

NASA Astrophysics Data System (ADS)

Tu, Bin; Xie, Yan; Zhang, Linbo; Lu, Benzhuo

2015-03-01

We have previously developed a finite element simulator, ichannel, to simulate ion transport through three-dimensional ion channel systems via solving the Poisson-Nernst-Planck equations (PNP) and Size-modified Poisson-Nernst-Planck equations (SMPNP), and succeeded in simulating some ion channel systems. However, the iterative solution between the coupled Poisson equation and the Nernst-Planck equations has difficulty converging for some large systems. One reason we found is that the NP equations are advection-dominated diffusion equations, which causes troubles in the usual FE solution. The stabilized schemes have been applied to compute fluids flow in various research fields. However, they have not been studied in the simulation of ion transport through three-dimensional models based on experimentally determined ion channel structures. In this paper, two stabilized techniques, the SUPG and the Pseudo Residual-Free Bubble function (PRFB) are introduced to enhance the numerical robustness and convergence performance of the finite element algorithm in ichannel. The conductances of the voltage dependent anion channel (VDAC) and the anthrax toxin protective antigen pore (PA) are simulated to validate the stabilization techniques. Those two stabilized schemes give reasonable results for the two proteins, with decent agreement with both experimental data and Brownian dynamics (BD) simulations. For a variety of numerical tests, it is found that the simulator effectively avoids previous numerical instability after introducing the stabilization methods. Comparison based on our test data set between the two stabilized schemes indicates both SUPG and PRFB have similar performance (the latter is slightly more accurate and stable), while SUPG is relatively more convenient to implement.

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.

A High Order Discontinuous Galerkin Method for 2D Incompressible Flows

NASA Technical Reports Server (NTRS)

Liu, Jia-Guo; Shu, Chi-Wang

1999-01-01

In this paper we introduce a high order discontinuous Galerkin method for two dimensional incompressible flow in vorticity streamfunction formulation. The momentum equation is treated explicitly, utilizing the efficiency of the discontinuous Galerkin method The streamfunction is obtained by a standard Poisson solver using continuous finite elements. There is a natural matching between these two finite element spaces, since the normal component of the velocity field is continuous across element boundaries. This allows for a correct upwinding gluing in the discontinuous Galerkin framework, while still maintaining total energy conservation with no numerical dissipation and total enstrophy stability The method is suitable for inviscid or high Reynolds number flows. Optimal error estimates are proven and verified by numerical experiments.

Transient finite element analysis of electric double layer using Nernst-Planck-Poisson equations with a modified Stern layer.

PubMed

Lim, Jongil; Whitcomb, John; Boyd, James; Varghese, Julian

2007-01-01

A finite element implementation of the transient nonlinear Nernst-Planck-Poisson (NPP) and Nernst-Planck-Poisson-modified Stern (NPPMS) models is presented. The NPPMS model uses multipoint constraints to account for finite ion size, resulting in realistic ion concentrations even at high surface potential. The Poisson-Boltzmann equation is used to provide a limited check of the transient models for low surface potential and dilute bulk solutions. The effects of the surface potential and bulk molarity on the electric potential and ion concentrations as functions of space and time are studied. The ability of the models to predict realistic energy storage capacity is investigated. The predicted energy is much more sensitive to surface potential than to bulk solution molarity.

Symmetries and Invariants of Twisted Quantum Algebras and Associated Poisson Algebras

NASA Astrophysics Data System (ADS)

Molev, A. I.; Ragoucy, E.

We construct an action of the braid group BN on the twisted quantized enveloping algebra U q'( {o}N) where the elements of BN act as automorphisms. In the classical limit q → 1, we recover the action of BN on the polynomial functions on the space of upper triangular matrices with ones on the diagonal. The action preserves the Poisson bracket on the space of polynomials which was introduced by Nelson and Regge in their study of quantum gravity and rediscovered in the mathematical literature. Furthermore, we construct a Poisson bracket on the space of polynomials associated with another twisted quantized enveloping algebra U q'( {sp}2n). We use the Casimir elements of both twisted quantized enveloping algebras to reproduce and construct some well-known and new polynomial invariants of the corresponding Poisson algebras.

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.

On the fractal characterization of Paretian Poisson processes

NASA Astrophysics Data System (ADS)

Eliazar, Iddo I.; Sokolov, Igor M.

2012-06-01

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

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

A fictitious domain approach for the Stokes problem based on the extended finite element method

NASA Astrophysics Data System (ADS)

Court, Sébastien; Fournié, Michel; Lozinski, Alexei

2014-01-01

In the present work, we propose to extend to the Stokes problem a fictitious domain approach inspired by eXtended Finite Element Method and studied for Poisson problem in [Renard]. The method allows computations in domains whose boundaries do not match. A mixed finite element method is used for fluid flow. The interface between the fluid and the structure is localized by a level-set function. Dirichlet boundary conditions are taken into account using Lagrange multiplier. A stabilization term is introduced to improve the approximation of the normal trace of the Cauchy stress tensor at the interface and avoid the inf-sup condition between the spaces for velocity and the Lagrange multiplier. Convergence analysis is given and several numerical tests are performed to illustrate the capabilities of the method.

Solving the MHD equations by the space time conservation element and solution element method

NASA Astrophysics Data System (ADS)

Zhang, Moujin; John Yu, S.-T.; Henry Lin, S.-C.; Chang, Sin-Chung; Blankson, Isaiah

2006-05-01

We apply the space-time conservation element and solution element (CESE) method to solve the ideal MHD equations with special emphasis on satisfying the divergence free constraint of magnetic field, i.e., ∇ · B = 0. In the setting of the CESE method, four approaches are employed: (i) the original CESE method without any additional treatment, (ii) a simple corrector procedure to update the spatial derivatives of magnetic field B after each time marching step to enforce ∇ · B = 0 at all mesh nodes, (iii) a constraint-transport method by using a special staggered mesh to calculate magnetic field B, and (iv) the projection method by solving a Poisson solver after each time marching step. To demonstrate the capabilities of these methods, two benchmark MHD flows are calculated: (i) a rotated one-dimensional MHD shock tube problem and (ii) a MHD vortex problem. The results show no differences between different approaches and all results compare favorably with previously reported data.

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.

The accuracy of the Gaussian-and-finite-element-Coulomb (GFC) method for the calculation of Coulomb integrals.

PubMed

Przybytek, Michal; Helgaker, Trygve

2013-08-07

We analyze the accuracy of the Coulomb energy calculated using the Gaussian-and-finite-element-Coulomb (GFC) method. In this approach, the electrostatic potential associated with the molecular electronic density is obtained by solving the Poisson equation and then used to calculate matrix elements of the Coulomb operator. The molecular electrostatic potential is expanded in a mixed Gaussian-finite-element (GF) basis set consisting of Gaussian functions of s symmetry centered on the nuclei (with exponents obtained from a full optimization of the atomic potentials generated by the atomic densities from symmetry-averaged restricted open-shell Hartree-Fock theory) and shape functions defined on uniform finite elements. The quality of the GF basis is controlled by means of a small set of parameters; for a given width of the finite elements d, the highest accuracy is achieved at smallest computational cost when tricubic (n = 3) elements are used in combination with two (γ(H) = 2) and eight (γ(1st) = 8) Gaussians on hydrogen and first-row atoms, respectively, with exponents greater than a given threshold (αmin (G)=0.5). The error in the calculated Coulomb energy divided by the number of atoms in the system depends on the system type but is independent of the system size or the orbital basis set, vanishing approximately like d(4) with decreasing d. If the boundary conditions for the Poisson equation are calculated in an approximate way, the GFC method may lose its variational character when the finite elements are too small; with larger elements, it is less sensitive to inaccuracies in the boundary values. As it is possible to obtain accurate boundary conditions in linear time, the overall scaling of the GFC method for large systems is governed by another computational step-namely, the generation of the three-center overlap integrals with three Gaussian orbitals. The most unfavorable (nearly quadratic) scaling is observed for compact, truly three-dimensional systems; however, this scaling can be reduced to linear by introducing more effective techniques for recognizing significant three-center overlap distributions.

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.

Continuum simulations of acetylcholine consumption by acetylcholinesterase: a Poisson-Nernst-Planck approach.

PubMed

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

2008-01-17

The Poisson-Nernst-Planck (PNP) equation provides a continuum description of electrostatic-driven diffusion and is used here to model the diffusion and reaction of acetylcholine (ACh) with acetylcholinesterase (AChE) enzymes. This study focuses on the effects of ion and substrate concentrations on the reaction rate and rate coefficient. To this end, the PNP equations are numerically solved with a hybrid finite element and boundary element method at a wide range of ion and substrate concentrations, and the results are compared with the partially coupled Smoluchowski-Poisson-Boltzmann model. The reaction rate is found to depend strongly on the concentrations of both the substrate and ions; this is explained by the competition between the intersubstrate repulsion and the ionic screening effects. The reaction rate coefficient is independent of the substrate concentration only at very high ion concentrations, whereas at low ion concentrations the behavior of the rate depends strongly on the substrate concentration. Moreover, at physiological ion concentrations, variations in substrate concentration significantly affect the transient behavior of the reaction. Our results offer a reliable estimate of reaction rates at various conditions and imply that the concentrations of charged substrates must be coupled with the electrostatic computation to provide a more realistic description of neurotransmission and other electrodiffusion and reaction processes.

Probabilistic structural analysis methods for improving Space Shuttle engine reliability

NASA Technical Reports Server (NTRS)

Boyce, L.

1989-01-01

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

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

PubMed

Xie, Yang; Ying, Jinyong; Xie, Dexuan

2017-03-30

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

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.

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.

Elastic properties and phase transitions of Fe7C3 and new constraints on the light element budget of the Earth's inner core

NASA Astrophysics Data System (ADS)

Prescher, C.; Bykova, E.; Kupenko, I.; Glazyrin, K.; Kantor, A.; McCammon, C. A.; Mookherjee, M.; Miyajima, N.; Cerantola, V.; Nakajima, Y.; Prakapenka, V.; Rüffer, R.; Chumakov, A.; Dubrovinsky, L. S.

2013-12-01

The Earth's inner core consists mainly of iron (or iron-nickel alloy) with some amount of light element(s) whereby their nature remains controversial. Seismological data suggest that the material forming Earth's inner core (pressures over 330 GPa and temperatures above 5000 K) has an enigmatically high Poisson's ratio ~0.44, while iron or it alloys with Si, S, O, or H expected to have at appropriate thermodynamic conditions Poisson's ratio well below 0.39. We will present an experimental study on a new high pressure variant in the iron carbide system. We have synthesized and solved structure of high-pressure orthorhombic phase of o-Fe7C3, and investigated its stability and behavior at pressures over 180 GPa and temperatures above 3500 K by means of different methods including single crystal X-ray diffraction, Mössbauer spectroscopy, and nuclear resonance scattering. O-Fe7C3 is structurally stable to at least outer core conditions and demonstrates magnetic or electronic transitions at ~18 GPa and ~70 GPa. The high pressure phase of o-Fe7C3 above 70 GPa exhibits anomalous elastic properties. When extrapolated to the conditions of the Earth's inner core it shows shear wave velocities and Poisson's ratios close to the values inferred by seismological models. Our results not only support earlier works suggesting that carbon may be an important component of Earth's core, but shows that it may drastically change iron's elastic properties, thus explaining anomalous Earth's inner core elastic properties.

An inelastic analysis of a welded aluminum joint

NASA Astrophysics Data System (ADS)

Vaughan, R. E.

1994-09-01

Butt-weld joints are most commonly designed into pressure vessels which then become as reliable as the weakest increment in the weld chain. In practice, weld material properties are determined from tensile test specimen and provided to the stress analyst in the form of a stress versus strain diagram. Variations in properties through the thickness of the weld and along the width of the weld have been suspect but not explored because of inaccessibility and cost. The purpose of this study is to investigate analytical and computational methods used for analysis of welds. The weld specimens are analyzed using classical elastic and plastic theory to provide a basis for modeling the inelastic properties in a finite-element solution. The results of the analysis are compared to experimental data to determine the weld behavior and the accuracy of prediction methods. The weld considered in this study is a multiple-pass aluminum 2219-T87 butt weld with thickness of 1.40 in. The weld specimen is modeled using the finite-element code ABAQUS. The finite-element model is used to produce the stress-strain behavior in the elastic and plastic regimes and to determine Poisson's ratio in the plastic region. The value of Poisson's ratio in the plastic regime is then compared to experimental data. The results of the comparisons are used to explain multipass weld behavior and to make recommendations concerning the analysis and testing of welds.

An inelastic analysis of a welded aluminum joint

NASA Technical Reports Server (NTRS)

Vaughan, R. E.

1994-01-01

Butt-weld joints are most commonly designed into pressure vessels which then become as reliable as the weakest increment in the weld chain. In practice, weld material properties are determined from tensile test specimen and provided to the stress analyst in the form of a stress versus strain diagram. Variations in properties through the thickness of the weld and along the width of the weld have been suspect but not explored because of inaccessibility and cost. The purpose of this study is to investigate analytical and computational methods used for analysis of welds. The weld specimens are analyzed using classical elastic and plastic theory to provide a basis for modeling the inelastic properties in a finite-element solution. The results of the analysis are compared to experimental data to determine the weld behavior and the accuracy of prediction methods. The weld considered in this study is a multiple-pass aluminum 2219-T87 butt weld with thickness of 1.40 in. The weld specimen is modeled using the finite-element code ABAQUS. The finite-element model is used to produce the stress-strain behavior in the elastic and plastic regimes and to determine Poisson's ratio in the plastic region. The value of Poisson's ratio in the plastic regime is then compared to experimental data. The results of the comparisons are used to explain multipass weld behavior and to make recommendations concerning the analysis and testing of welds.

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

PubMed

de Nijs, Robin

2015-07-21

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

Coupling Finite Element and Meshless Local Petrov-Galerkin Methods for Two-Dimensional Potential Problems

NASA Technical Reports Server (NTRS)

Chen, T.; Raju, I. S.

2002-01-01

A coupled finite element (FE) method and meshless local Petrov-Galerkin (MLPG) method for analyzing two-dimensional potential problems is presented in this paper. The analysis domain is subdivided into two regions, a finite element (FE) region and a meshless (MM) region. A single weighted residual form is written for the entire domain. Independent trial and test functions are assumed in the FE and MM regions. A transition region is created between the two regions. The transition region blends the trial and test functions of the FE and MM regions. The trial function blending is achieved using a technique similar to the 'Coons patch' method that is widely used in computer-aided geometric design. The test function blending is achieved by using either FE or MM test functions on the nodes in the transition element. The technique was evaluated by applying the coupled method to two potential problems governed by the Poisson equation. The coupled method passed all the patch test problems and gave accurate solutions for the problems studied.

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

NASA Technical Reports Server (NTRS)

Van Dommelen, Leon; Rundensteiner, Elke A.

1989-01-01

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

The NonConforming Virtual Element Method for the Stokes Equations

DOE PAGES

Cangiani, Andrea; Gyrya, Vitaliy; Manzini, Gianmarco

2016-01-01

In this paper, we present the nonconforming virtual element method (VEM) for the numerical approximation of velocity and pressure in the steady Stokes problem. The pressure is approximated using discontinuous piecewise polynomials, while each component of the velocity is approximated using the nonconforming virtual element space. On each mesh element the local virtual space contains the space of polynomials of up to a given degree, plus suitable nonpolynomial functions. The virtual element functions are implicitly defined as the solution of local Poisson problems with polynomial Neumann boundary conditions. As typical in VEM approaches, the explicit evaluation of the non-polynomial functionsmore » is not required. This approach makes it possible to construct nonconforming (virtual) spaces for any polynomial degree regardless of the parity, for two- and three-dimensional problems, and for meshes with very general polygonal and polyhedral elements. We show that the nonconforming VEM is inf-sup stable and establish optimal a priori error estimates for the velocity and pressure approximations. Finally, numerical examples confirm the convergence analysis and the effectiveness of the method in providing high-order accurate approximations.« less

Preconditioned Mixed Spectral Element Methods for Elasticity and Stokes Problems

NASA Technical Reports Server (NTRS)

Pavarino, Luca F.

1996-01-01

Preconditioned iterative methods for the indefinite systems obtained by discretizing the linear elasticity and Stokes problems with mixed spectral elements in three dimensions are introduced and analyzed. The resulting stiffness matrices have the structure of saddle point problems with a penalty term, which is associated with the Poisson ratio for elasticity problems or with stabilization techniques for Stokes problems. The main results of this paper show that the convergence rate of the resulting algorithms is independent of the penalty parameter, the number of spectral elements Nu and mildly dependent on the spectral degree eta via the inf-sup constant. The preconditioners proposed for the whole indefinite system are block-diagonal and block-triangular. Numerical experiments presented in the final section show that these algorithms are a practical and efficient strategy for the iterative solution of the indefinite problems arising from mixed spectral element discretizations of elliptic systems.

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

NASA Astrophysics Data System (ADS)

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

2016-05-01

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

Method for resonant measurement

DOEpatents

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

1996-03-05

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

Solving the Helmholtz equation in conformal mapped ARROW structures using homotopy perturbation method.

PubMed

Reck, Kasper; Thomsen, Erik V; Hansen, Ole

2011-01-31

The scalar wave equation, or Helmholtz equation, describes within a certain approximation the electromagnetic field distribution in a given system. In this paper we show how to solve the Helmholtz equation in complex geometries using conformal mapping and the homotopy perturbation method. The solution of the mapped Helmholtz equation is found by solving an infinite series of Poisson equations using two dimensional Fourier series. The solution is entirely based on analytical expressions and is not mesh dependent. The analytical results are compared to a numerical (finite element method) solution.

Simulation Methods for Poisson Processes in Nonstationary Systems.

DTIC Science & Technology

1978-08-01

for simulation of nonhomogeneous Poisson processes is stated with log-linear rate function. The method is based on an identity relating the...and relatively efficient new method for simulation of one-dimensional and two-dimensional nonhomogeneous Poisson processes is described. The method is

An adaptive grid scheme using the boundary element method

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

Munipalli, R.; Anderson, D.A.

1996-09-01

A technique to solve the Poisson grid generation equations by Green`s function related methods has been proposed, with the source terms being purely position dependent. The use of distributed singularities in the flow domain coupled with the boundary element method (BEM) formulation is presented in this paper as a natural extension of the Green`s function method. This scheme greatly simplifies the adaption process. The BEM reduces the dimensionality of the given problem by one. Internal grid-point placement can be achieved for a given boundary distribution by adding continuous and discrete source terms in the BEM formulation. A distribution of vortexmore » doublets is suggested as a means of controlling grid-point placement and grid-line orientation. Examples for sample adaption problems are presented and discussed. 15 refs., 20 figs.« less

Mesh Deformation Based on Fully Stressed Design: The Method and Two-Dimensional Examples

NASA Technical Reports Server (NTRS)

Hsu, Su-Yuen; Chang, Chau-Lyan

2007-01-01

Mesh deformation in response to redefined boundary geometry is a frequently encountered task in shape optimization and analysis of fluid-structure interaction. We propose a simple and concise method for deforming meshes defined with three-node triangular or four-node tetrahedral elements. The mesh deformation method is suitable for large boundary movement. The approach requires two consecutive linear elastic finite-element analyses of an isotropic continuum using a prescribed displacement at the mesh boundaries. The first analysis is performed with homogeneous elastic property and the second with inhomogeneous elastic property. The fully stressed design is employed with a vanishing Poisson s ratio and a proposed form of equivalent strain (modified Tresca equivalent strain) to calculate, from the strain result of the first analysis, the element-specific Young s modulus for the second analysis. The theoretical aspect of the proposed method, its convenient numerical implementation using a typical linear elastic finite-element code in conjunction with very minor extra coding for data processing, and results for examples of large deformation of two-dimensional meshes are presented in this paper. KEY WORDS: Mesh deformation, shape optimization, fluid-structure interaction, fully stressed design, finite-element analysis, linear elasticity, strain failure, equivalent strain, Tresca failure criterion

Critical elements on fitting the Bayesian multivariate Poisson Lognormal model

NASA Astrophysics Data System (ADS)

Zamzuri, Zamira Hasanah binti

2015-10-01

Motivated by a problem on fitting multivariate models to traffic accident data, a detailed discussion of the Multivariate Poisson Lognormal (MPL) model is presented. This paper reveals three critical elements on fitting the MPL model: the setting of initial estimates, hyperparameters and tuning parameters. These issues have not been highlighted in the literature. Based on simulation studies conducted, we have shown that to use the Univariate Poisson Model (UPM) estimates as starting values, at least 20,000 iterations are needed to obtain reliable final estimates. We also illustrated the sensitivity of the specific hyperparameter, which if it is not given extra attention, may affect the final estimates. The last issue is regarding the tuning parameters where they depend on the acceptance rate. Finally, a heuristic algorithm to fit the MPL model is presented. This acts as a guide to ensure that the model works satisfactorily given any data set.

Calculation of the Poisson cumulative distribution function

NASA Technical Reports Server (NTRS)

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

1990-01-01

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

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.

Analysis and control of hourglass instabilities in underintegrated linear and nonlinear elasticity

NASA Technical Reports Server (NTRS)

Jacquotte, Olivier P.; Oden, J. Tinsley

1994-01-01

Methods are described to identify and correct a bad finite element approximation of the governing operator obtained when under-integration is used in numerical code for several model problems: the Poisson problem, the linear elasticity problem, and for problems in the nonlinear theory of elasticity. For each of these problems, the reason for the occurrence of instabilities is given, a way to control or eliminate them is presented, and theorems of existence, uniqueness, and convergence for the given methods are established. Finally, numerical results are included which illustrate the theory.

Calculation of ionized fields in DC electrostatic precipitators in the presence of dust and electric wind

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

Cristina, S.; Feliziani, M.

1995-11-01

This paper describes a new procedure for the numerical computation of the electric field and current density distributions in a dc electrostatic precipitator in the presence of dust, taking into account the particle-size distribution. Poisson`s and continuity equations are numerically solved by supposing that the coronating conductors satisfy Kaptzov`s assumption on the emitter surfaces. Two iterative numerical procedures, both based on the finite element method (FEM), are implemented for evaluating, respectively, the unknown ionic charge density and the particle charge density distributions. The V-I characteristic and the precipitation efficiencies for the individual particle-size classes, calculated with reference to the pilotmore » precipitator installed by ENEL (Italian Electricity Board) at its Marghera (Venice) coal-fired power station, are found to be very close to those measured experimentally.« less

Effect of Poisson's loss factor of rubbery material on underwater sound absorption of anechoic coatings

NASA Astrophysics Data System (ADS)

Zhong, Jie; Zhao, Honggang; Yang, Haibin; Yin, Jianfei; Wen, Jihong

2018-06-01

Rubbery coatings embedded with air cavities are commonly used on underwater structures to reduce reflection of incoming sound waves. In this paper, the relationships between Poisson's and modulus loss factors of rubbery materials are theoretically derived, the different effects of the tiny Poisson's loss factor on characterizing the loss factors of shear and longitudinal moduli are revealed. Given complex Young's modulus and dynamic Poisson's ratio, it is found that the shear loss factor has almost invisible variation with the Poisson's loss factor and is very close to the loss factor of Young's modulus, while the longitudinal loss factor almost linearly decreases with the increase of Poisson's loss factor. Then, a finite element (FE) model is used to investigate the effect of the tiny Poisson's loss factor, which is generally neglected in some FE models, on the underwater sound absorption of rubbery coatings. Results show that the tiny Poisson's loss factor has a significant effect on the sound absorption of homogeneous coatings within the concerned frequency range, while it has both frequency- and structure-dependent influence on the sound absorption of inhomogeneous coatings with embedded air cavities. Given the material parameters and cavity dimensions, more obvious effect can be observed for the rubbery coating with a larger lattice constant and/or a thicker cover layer.

Anisotropic norm-oriented mesh adaptation for a Poisson problem

NASA Astrophysics Data System (ADS)

Brèthes, Gautier; Dervieux, Alain

2016-10-01

We present a novel formulation for the mesh adaptation of the approximation of a Partial Differential Equation (PDE). The discussion is restricted to a Poisson problem. The proposed norm-oriented formulation extends the goal-oriented formulation since it is equation-based and uses an adjoint. At the same time, the norm-oriented formulation somewhat supersedes the goal-oriented one since it is basically a solution-convergent method. Indeed, goal-oriented methods rely on the reduction of the error in evaluating a chosen scalar output with the consequence that, as mesh size is increased (more degrees of freedom), only this output is proven to tend to its continuous analog while the solution field itself may not converge. A remarkable quality of goal-oriented metric-based adaptation is the mathematical formulation of the mesh adaptation problem under the form of the optimization, in the well-identified set of metrics, of a well-defined functional. In the new proposed formulation, we amplify this advantage. We search, in the same well-identified set of metrics, the minimum of a norm of the approximation error. The norm is prescribed by the user and the method allows addressing the case of multi-objective adaptation like, for example in aerodynamics, adaptating the mesh for drag, lift and moment in one shot. In this work, we consider the basic linear finite-element approximation and restrict our study to L2 norm in order to enjoy second-order convergence. Numerical examples for the Poisson problem are computed.

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

Cangiani, Andrea; Gyrya, Vitaliy; Manzini, Gianmarco

In this paper, we present the nonconforming virtual element method (VEM) for the numerical approximation of velocity and pressure in the steady Stokes problem. The pressure is approximated using discontinuous piecewise polynomials, while each component of the velocity is approximated using the nonconforming virtual element space. On each mesh element the local virtual space contains the space of polynomials of up to a given degree, plus suitable nonpolynomial functions. The virtual element functions are implicitly defined as the solution of local Poisson problems with polynomial Neumann boundary conditions. As typical in VEM approaches, the explicit evaluation of the non-polynomial functionsmore » is not required. This approach makes it possible to construct nonconforming (virtual) spaces for any polynomial degree regardless of the parity, for two- and three-dimensional problems, and for meshes with very general polygonal and polyhedral elements. We show that the nonconforming VEM is inf-sup stable and establish optimal a priori error estimates for the velocity and pressure approximations. Finally, numerical examples confirm the convergence analysis and the effectiveness of the method in providing high-order accurate approximations.« less

Poisson pre-processing of nonstationary photonic signals: Signals with equality between mean and variance.

PubMed

Poplová, Michaela; Sovka, Pavel; Cifra, Michal

2017-01-01

Photonic signals are broadly exploited in communication and sensing and they typically exhibit Poisson-like statistics. In a common scenario where the intensity of the photonic signals is low and one needs to remove a nonstationary trend of the signals for any further analysis, one faces an obstacle: due to the dependence between the mean and variance typical for a Poisson-like process, information about the trend remains in the variance even after the trend has been subtracted, possibly yielding artifactual results in further analyses. Commonly available detrending or normalizing methods cannot cope with this issue. To alleviate this issue we developed a suitable pre-processing method for the signals that originate from a Poisson-like process. In this paper, a Poisson pre-processing method for nonstationary time series with Poisson distribution is developed and tested on computer-generated model data and experimental data of chemiluminescence from human neutrophils and mung seeds. The presented method transforms a nonstationary Poisson signal into a stationary signal with a Poisson distribution while preserving the type of photocount distribution and phase-space structure of the signal. The importance of the suggested pre-processing method is shown in Fano factor and Hurst exponent analysis of both computer-generated model signals and experimental photonic signals. It is demonstrated that our pre-processing method is superior to standard detrending-based methods whenever further signal analysis is sensitive to variance of the signal.

Poisson pre-processing of nonstationary photonic signals: Signals with equality between mean and variance

PubMed Central

Poplová, Michaela; Sovka, Pavel

2017-01-01

Photonic signals are broadly exploited in communication and sensing and they typically exhibit Poisson-like statistics. In a common scenario where the intensity of the photonic signals is low and one needs to remove a nonstationary trend of the signals for any further analysis, one faces an obstacle: due to the dependence between the mean and variance typical for a Poisson-like process, information about the trend remains in the variance even after the trend has been subtracted, possibly yielding artifactual results in further analyses. Commonly available detrending or normalizing methods cannot cope with this issue. To alleviate this issue we developed a suitable pre-processing method for the signals that originate from a Poisson-like process. In this paper, a Poisson pre-processing method for nonstationary time series with Poisson distribution is developed and tested on computer-generated model data and experimental data of chemiluminescence from human neutrophils and mung seeds. The presented method transforms a nonstationary Poisson signal into a stationary signal with a Poisson distribution while preserving the type of photocount distribution and phase-space structure of the signal. The importance of the suggested pre-processing method is shown in Fano factor and Hurst exponent analysis of both computer-generated model signals and experimental photonic signals. It is demonstrated that our pre-processing method is superior to standard detrending-based methods whenever further signal analysis is sensitive to variance of the signal. PMID:29216207

Numerical Methods of Computational Electromagnetics for Complex Inhomogeneous Systems

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

Cai, Wei

Understanding electromagnetic phenomena is the key in many scientific investigation and engineering designs such as solar cell designs, studying biological ion channels for diseases, and creating clean fusion energies, among other things. The objectives of the project are to develop high order numerical methods to simulate evanescent electromagnetic waves occurring in plasmon solar cells and biological ion-channels, where local field enhancement within random media in the former and long range electrostatic interactions in the latter are of major challenges for accurate and efficient numerical computations. We have accomplished these objectives by developing high order numerical methods for solving Maxwell equationsmore » such as high order finite element basis for discontinuous Galerkin methods, well-conditioned Nedelec edge element method, divergence free finite element basis for MHD, and fast integral equation methods for layered media. These methods can be used to model the complex local field enhancement in plasmon solar cells. On the other hand, to treat long range electrostatic interaction in ion channels, we have developed image charge based method for a hybrid model in combining atomistic electrostatics and continuum Poisson-Boltzmann electrostatics. Such a hybrid model will speed up the molecular dynamics simulation of transport in biological ion-channels.« less

Mechanics of fiber reinforced materials

NASA Astrophysics Data System (ADS)

Sun, Huiyu

This dissertation is dedicated to mechanics of fiber reinforced materials and the woven reinforcement and composed of four parts of research: analytical characterization of the interfaces in laminated composites; micromechanics of braided composites; shear deformation, and Poisson's ratios of woven fabric reinforcements. A new approach to evaluate the mechanical characteristics of interfaces between composite laminae based on a modified laminate theory is proposed. By including an interface as a special lamina termed the "bonding-layer" in the analysis, the mechanical properties of the interfaces are obtained. A numerical illustration is given. For micro-mechanical properties of three-dimensionally braided composite materials, a new method via homogenization theory and incompatible multivariable FEM is developed. Results from the hybrid stress element approach compare more favorably with the experimental data than other existing numerical methods widely used. To evaluate the shearing properties for woven fabrics, a new mechanical model is proposed during the initial slip region. Analytical results show that this model provides better agreement with the experiments for both the initial shear modulus and the slipping angle than the existing models. Finally, another mechanical model for a woven fabric made of extensible yarns is employed to calculate the fabric Poisson's ratios. Theoretical results are compared with the available experimental data. A thorough examination on the influences of various mechanical properties of yarns and structural parameters of fabrics on the Poisson's ratios of a woven fabric is given at the end.

A Method of Poisson's Ration Imaging Within a Material Part

NASA Technical Reports Server (NTRS)

Roth, Don J. (Inventor)

1994-01-01

The present invention is directed to a method of displaying the Poisson's ratio image of a material part. In the present invention, longitudinal data is produced using a longitudinal wave transducer and shear wave data is produced using a shear wave transducer. The respective data is then used to calculate the Poisson's ratio for the entire material part. The Poisson's ratio approximations are then used to display the data.

Method of Poisson's ratio imaging within a material part

NASA Technical Reports Server (NTRS)

Roth, Don J. (Inventor)

1996-01-01

The present invention is directed to a method of displaying the Poisson's ratio image of a material part. In the present invention longitudinal data is produced using a longitudinal wave transducer and shear wave data is produced using a shear wave transducer. The respective data is then used to calculate the Poisson's ratio for the entire material part. The Poisson's ratio approximations are then used to displayed the image.

Paretian Poisson Processes

NASA Astrophysics Data System (ADS)

Eliazar, Iddo; Klafter, Joseph

2008-05-01

Many random populations can be modeled as a countable set of points scattered randomly on the positive half-line. The points may represent magnitudes of earthquakes and tornados, masses of stars, market values of public companies, etc. In this article we explore a specific class of random such populations we coin ` Paretian Poisson processes'. This class is elemental in statistical physics—connecting together, in a deep and fundamental way, diverse issues including: the Poisson distribution of the Law of Small Numbers; Paretian tail statistics; the Fréchet distribution of Extreme Value Theory; the one-sided Lévy distribution of the Central Limit Theorem; scale-invariance, renormalization and fractality; resilience to random perturbations.

Modeling Electrokinetic Flows by the Smoothed Profile Method

PubMed Central

Luo, Xian; Beskok, Ali; Karniadakis, George Em

2010-01-01

We propose an efficient modeling method for electrokinetic flows based on the Smoothed Profile Method (SPM) [1–4] and spectral element discretizations. The new method allows for arbitrary differences in the electrical conductivities between the charged surfaces and the the surrounding electrolyte solution. The electrokinetic forces are included into the flow equations so that the Poisson-Boltzmann and electric charge continuity equations are cast into forms suitable for SPM. The method is validated by benchmark problems of electroosmotic flow in straight channels and electrophoresis of charged cylinders. We also present simulation results of electrophoresis of charged microtubules, and show that the simulated electrophoretic mobility and anisotropy agree with the experimental values. PMID:20352076

ADAPTIVE FINITE ELEMENT MODELING TECHNIQUES FOR THE POISSON-BOLTZMANN EQUATION

PubMed Central

HOLST, MICHAEL; MCCAMMON, JAMES ANDREW; YU, ZEYUN; ZHOU, YOUNGCHENG; ZHU, YUNRONG

2011-01-01

We consider the design of an effective and reliable adaptive finite element method (AFEM) for the nonlinear Poisson-Boltzmann equation (PBE). We first examine the two-term regularization technique for the continuous problem recently proposed by Chen, Holst, and Xu based on the removal of the singular electrostatic potential inside biomolecules; this technique made possible the development of the first complete solution and approximation theory for the Poisson-Boltzmann equation, the first provably convergent discretization, and also allowed for the development of a provably convergent AFEM. However, in practical implementation, this two-term regularization exhibits numerical instability. Therefore, we examine a variation of this regularization technique which can be shown to be less susceptible to such instability. We establish a priori estimates and other basic results for the continuous regularized problem, as well as for Galerkin finite element approximations. We show that the new approach produces regularized continuous and discrete problems with the same mathematical advantages of the original regularization. We then design an AFEM scheme for the new regularized problem, and show that the resulting AFEM scheme is accurate and reliable, by proving a contraction result for the error. This result, which is one of the first results of this type for nonlinear elliptic problems, is based on using continuous and discrete a priori L∞ estimates to establish quasi-orthogonality. To provide a high-quality geometric model as input to the AFEM algorithm, we also describe a class of feature-preserving adaptive mesh generation algorithms designed specifically for constructing meshes of biomolecular structures, based on the intrinsic local structure tensor of the molecular surface. All of the algorithms described in the article are implemented in the Finite Element Toolkit (FETK), developed and maintained at UCSD. The stability advantages of the new regularization scheme are demonstrated with FETK through comparisons with the original regularization approach for a model problem. The convergence and accuracy of the overall AFEM algorithm is also illustrated by numerical approximation of electrostatic solvation energy for an insulin protein. PMID:21949541

Performance of the modified Poisson regression approach for estimating relative risks from clustered prospective data.

PubMed

Yelland, Lisa N; Salter, Amy B; Ryan, Philip

2011-10-15

Modified Poisson regression, which combines a log Poisson regression model with robust variance estimation, is a useful alternative to log binomial regression for estimating relative risks. Previous studies have shown both analytically and by simulation that modified Poisson regression is appropriate for independent prospective data. This method is often applied to clustered prospective data, despite a lack of evidence to support its use in this setting. The purpose of this article is to evaluate the performance of the modified Poisson regression approach for estimating relative risks from clustered prospective data, by using generalized estimating equations to account for clustering. A simulation study is conducted to compare log binomial regression and modified Poisson regression for analyzing clustered data from intervention and observational studies. Both methods generally perform well in terms of bias, type I error, and coverage. Unlike log binomial regression, modified Poisson regression is not prone to convergence problems. The methods are contrasted by using example data sets from 2 large studies. The results presented in this article support the use of modified Poisson regression as an alternative to log binomial regression for analyzing clustered prospective data when clustering is taken into account by using generalized estimating equations.

On the extraction of pressure fields from PIV velocity measurements in turbines

NASA Astrophysics Data System (ADS)

Villegas, Arturo; Diez, Fancisco J.

2012-11-01

In this study, the pressure field for a water turbine is derived from particle image velocimetry (PIV) measurements. Measurements are performed in a recirculating water channel facility. The PIV measurements include calculating the tangential and axial forces applied to the turbine by solving the integral momentum equation around the airfoil. The results are compared with the forces obtained from the Blade Element Momentum theory (BEMT). Forces are calculated by using three different methods. In the first method, the pressure fields are obtained from PIV velocity fields by solving the Poisson equation. The boundary conditions are obtained from the Navier-Stokes momentum equations. In the second method, the pressure at the boundaries is determined by spatial integration of the pressure gradients along the boundaries. In the third method, applicable only to incompressible, inviscid, irrotational, and steady flow, the pressure is calculated using the Bernoulli equation. This approximated pressure is known to be accurate far from the airfoil and outside of the wake for steady flows. Additionally, the pressure is used to solve for the force from the integral momentum equation on the blade. From the three methods proposed to solve for pressure and forces from PIV measurements, the first one, which is solved by using the Poisson equation, provides the best match to the BEM theory calculations.

Application of p-Multigrid to Discontinuous Galerkin Formulations of the Poisson Equation

NASA Technical Reports Server (NTRS)

Helenbrook, B. T.; Atkins, H. L.

2006-01-01

We investigate p-multigrid as a solution method for several different discontinuous Galerkin (DG) formulations of the Poisson equation. Different combinations of relaxation schemes and basis sets have been combined with the DG formulations to find the best performing combination. The damping factors of the schemes have been determined using Fourier analysis for both one and two-dimensional problems. One important finding is that when using DG formulations, the standard approach of forming the coarse p matrices separately for each level of multigrid is often unstable. To ensure stability the coarse p matrices must be constructed from the fine grid matrices using algebraic multigrid techniques. Of the relaxation schemes, we find that the combination of Jacobi relaxation with the spectral element basis is fairly effective. The results using this combination are p sensitive in both one and two dimensions, but reasonable convergence rates can still be achieved for moderate values of p and isotropic meshes. A competitive alternative is a block Gauss-Seidel relaxation. This actually out performs a more expensive line relaxation when the mesh is isotropic. When the mesh becomes highly anisotropic, the implicit line method and the Gauss-Seidel implicit line method are the only effective schemes. Adding the Gauss-Seidel terms to the implicit line method gives a significant improvement over the line relaxation method.

HFEM3D

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

Weiss, Chester J

Software solves the three-dimensional Poisson equation div(k(grad(u)) = f, by the finite element method for the case when material properties, k, are distributed over hierarchy of edges, facets and tetrahedra in the finite element mesh. Method is described in Weiss, CJ, Finite element analysis for model parameters distributed on a hierarchy of geometric simplices, Geophysics, v82, E155-167, doi:10.1190/GEO2017-0058.1 (2017). A standard finite element method for solving Poisson’s equation is augmented by including in the 3D stiffness matrix additional 2D and 1D stiffness matrices representing the contributions from material properties associated with mesh faces and edges, respectively. The resulting linear systemmore » is solved iteratively using the conjugate gradient method with Jacobi preconditioning. To minimize computer storage for program execution, the linear solver computes matrix-vector contractions element-by-element over the mesh, without explicit storage of the global stiffness matrix. Program output vtk compliant for visualization and rendering by 3rd party software. Program uses dynamic memory allocation and as such there are no hard limits on problem size outside of those imposed by the operating system and configuration on which the software is run. Dimension, N, of the finite element solution vector is constrained by the the addressable space in 32-vs-64 bit operating systems. Total storage requirements for the problem. Total working space required for the program is approximately 13*N double precision words.« less

STIR: Improved Electrolyte Surface Exchange via Atomically Strained Surfaces

DTIC Science & Technology

2015-09-03

at the University of Delaware. Concomitant with the experimental work, we also conducted numerical simulations of the experiments. A Poisson- Nernst ...oxygen ion lattice site results in a reaction volume and an associated Vex·ΔP term in the Arrhenius rate equation . In addition, tensile strain (i.e...simulations of the experiments. In recent work at the University of Delaware [9-13], we used finite element solution of generalized Poisson- Nernst -Planck

BOOK REVIEW: Advanced Topics in Computational Partial Differential Equations: Numerical Methods and Diffpack Programming

NASA Astrophysics Data System (ADS)

Katsaounis, T. D.

2005-02-01

The scope of this book is to present well known simple and advanced numerical methods for solving partial differential equations (PDEs) and how to implement these methods using the programming environment of the software package Diffpack. A basic background in PDEs and numerical methods is required by the potential reader. Further, a basic knowledge of the finite element method and its implementation in one and two space dimensions is required. The authors claim that no prior knowledge of the package Diffpack is required, which is true, but the reader should be at least familiar with an object oriented programming language like C++ in order to better comprehend the programming environment of Diffpack. Certainly, a prior knowledge or usage of Diffpack would be a great advantage to the reader. The book consists of 15 chapters, each one written by one or more authors. Each chapter is basically divided into two parts: the first part is about mathematical models described by PDEs and numerical methods to solve these models and the second part describes how to implement the numerical methods using the programming environment of Diffpack. Each chapter closes with a list of references on its subject. The first nine chapters cover well known numerical methods for solving the basic types of PDEs. Further, programming techniques on the serial as well as on the parallel implementation of numerical methods are also included in these chapters. The last five chapters are dedicated to applications, modelled by PDEs, in a variety of fields. The first chapter is an introduction to parallel processing. It covers fundamentals of parallel processing in a simple and concrete way and no prior knowledge of the subject is required. Examples of parallel implementation of basic linear algebra operations are presented using the Message Passing Interface (MPI) programming environment. Here, some knowledge of MPI routines is required by the reader. Examples solving in parallel simple PDEs using Diffpack and MPI are also presented. Chapter 2 presents the overlapping domain decomposition method for solving PDEs. It is well known that these methods are suitable for parallel processing. The first part of the chapter covers the mathematical formulation of the method as well as algorithmic and implementational issues. The second part presents a serial and a parallel implementational framework within the programming environment of Diffpack. The chapter closes by showing how to solve two application examples with the overlapping domain decomposition method using Diffpack. Chapter 3 is a tutorial about how to incorporate the multigrid solver in Diffpack. The method is illustrated by examples such as a Poisson solver, a general elliptic problem with various types of boundary conditions and a nonlinear Poisson type problem. In chapter 4 the mixed finite element is introduced. Technical issues concerning the practical implementation of the method are also presented. The main difficulties of the efficient implementation of the method, especially in two and three space dimensions on unstructured grids, are presented and addressed in the framework of Diffpack. The implementational process is illustrated by two examples, namely the system formulation of the Poisson problem and the Stokes problem. Chapter 5 is closely related to chapter 4 and addresses the problem of how to solve efficiently the linear systems arising by the application of the mixed finite element method. The proposed method is block preconditioning. Efficient techniques for implementing the method within Diffpack are presented. Optimal block preconditioners are used to solve the system formulation of the Poisson problem, the Stokes problem and the bidomain model for the electrical activity in the heart. The subject of chapter 6 is systems of PDEs. Linear and nonlinear systems are discussed. Fully implicit and operator splitting methods are presented. Special attention is paid to how existing solvers for scalar equations in Diffpack can be used to derive fully implicit solvers for systems. The proposed techniques are illustrated in terms of two applications, namely a system of PDEs modelling pipeflow and a two-phase porous media flow. Stochastic PDEs is the topic of chapter 7. The first part of the chapter is a simple introduction to stochastic PDEs; basic analytical properties are presented for simple models like transport phenomena and viscous drag forces. The second part considers the numerical solution of stochastic PDEs. Two basic techniques are presented, namely Monte Carlo and perturbation methods. The last part explains how to implement and incorporate these solvers into Diffpack. Chapter 8 describes how to operate Diffpack from Python scripts. The main goal here is to provide all the programming and technical details in order to glue the programming environment of Diffpack with visualization packages through Python and in general take advantage of the Python interfaces. Chapter 9 attempts to show how to use numerical experiments to measure the performance of various PDE solvers. The authors gathered a rather impressive list, a total of 14 PDE solvers. Solvers for problems like Poisson, Navier--Stokes, elasticity, two-phase flows and methods such as finite difference, finite element, multigrid, and gradient type methods are presented. The authors provide a series of numerical results combining various solvers with various methods in order to gain insight into their computational performance and efficiency. In Chapter 10 the authors consider a computationally challenging problem, namely the computation of the electrical activity of the human heart. After a brief introduction on the biology of the problem the authors present the mathematical models involved and a numerical method for solving them within the framework of Diffpack. Chapter 11 and 12 are closely related; actually they could have been combined in a single chapter. Chapter 11 introduces several mathematical models used in finance, based on the Black--Scholes equation. Chapter 12 considers several numerical methods like Monte Carlo, lattice methods, finite difference and finite element methods. Implementation of these methods within Diffpack is presented in the last part of the chapter. Chapter 13 presents how the finite element method is used for the modelling and analysis of elastic structures. The authors describe the structural elements of Diffpack which include popular elements such as beams and plates and examples are presented on how to use them to simulate elastic structures. Chapter 14 describes an application problem, namely the extrusion of aluminum. This is a rather\\endcolumn complicated process which involves non-Newtonian flow, heat transfer and elasticity. The authors describe the systems of PDEs modelling the underlying process and use a finite element method to obtain a numerical solution. The implementation of the numerical method in Diffpack is presented along with some applications. The last chapter, chapter 15, focuses on mathematical and numerical models of systems of PDEs governing geological processes in sedimentary basins. The underlying mathematical model is solved using the finite element method within a fully implicit scheme. The authors discuss the implementational issues involved within Diffpack and they present results from several examples. In summary, the book focuses on the computational and implementational issues involved in solving partial differential equations. The potential reader should have a basic knowledge of PDEs and the finite difference and finite element methods. The examples presented are solved within the programming framework of Diffpack and the reader should have prior experience with the particular software in order to take full advantage of the book. Overall the book is well written, the subject of each chapter is well presented and can serve as a reference for graduate students, researchers and engineers who are interested in the numerical solution of partial differential equations modelling various applications.

Effective implementation of wavelet Galerkin method

NASA Astrophysics Data System (ADS)

Finěk, Václav; Šimunková, Martina

2012-11-01

It was proved by W. Dahmen et al. that an adaptive wavelet scheme is asymptotically optimal for a wide class of elliptic equations. This scheme approximates the solution u by a linear combination of N wavelets and a benchmark for its performance is the best N-term approximation, which is obtained by retaining the N largest wavelet coefficients of the unknown solution. Moreover, the number of arithmetic operations needed to compute the approximate solution is proportional to N. The most time consuming part of this scheme is the approximate matrix-vector multiplication. In this contribution, we will introduce our implementation of wavelet Galerkin method for Poisson equation -Δu = f on hypercube with homogeneous Dirichlet boundary conditions. In our implementation, we identified nonzero elements of stiffness matrix corresponding to the above problem and we perform matrix-vector multiplication only with these nonzero elements.

A test of inflated zeros for Poisson regression models.

PubMed

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

2017-01-01

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

Quantification of integrated HIV DNA by repetitive-sampling Alu-HIV PCR on the basis of poisson statistics.

PubMed

De Spiegelaere, Ward; Malatinkova, Eva; Lynch, Lindsay; Van Nieuwerburgh, Filip; Messiaen, Peter; O'Doherty, Una; Vandekerckhove, Linos

2014-06-01

Quantification of integrated proviral HIV DNA by repetitive-sampling Alu-HIV PCR is a candidate virological tool to monitor the HIV reservoir in patients. However, the experimental procedures and data analysis of the assay are complex and hinder its widespread use. Here, we provide an improved and simplified data analysis method by adopting binomial and Poisson statistics. A modified analysis method on the basis of Poisson statistics was used to analyze the binomial data of positive and negative reactions from a 42-replicate Alu-HIV PCR by use of dilutions of an integration standard and on samples of 57 HIV-infected patients. Results were compared with the quantitative output of the previously described Alu-HIV PCR method. Poisson-based quantification of the Alu-HIV PCR was linearly correlated with the standard dilution series, indicating that absolute quantification with the Poisson method is a valid alternative for data analysis of repetitive-sampling Alu-HIV PCR data. Quantitative outputs of patient samples assessed by the Poisson method correlated with the previously described Alu-HIV PCR analysis, indicating that this method is a valid alternative for quantifying integrated HIV DNA. Poisson-based analysis of the Alu-HIV PCR data enables absolute quantification without the need of a standard dilution curve. Implementation of the CI estimation permits improved qualitative analysis of the data and provides a statistical basis for the required minimal number of technical replicates. © 2014 The American Association for Clinical Chemistry.

Finite element model predictions of static deformation from dislocation sources in a subduction zone: Sensitivities to homogeneous, isotropic, Poisson-solid, and half-space assumptions

USGS Publications Warehouse

Masterlark, Timothy

2003-01-01

Dislocation models can simulate static deformation caused by slip along a fault. These models usually take the form of a dislocation embedded in a homogeneous, isotropic, Poisson-solid half-space (HIPSHS). However, the widely accepted HIPSHS assumptions poorly approximate subduction zone systems of converging oceanic and continental crust. This study uses three-dimensional finite element models (FEMs) that allow for any combination (including none) of the HIPSHS assumptions to compute synthetic Green's functions for displacement. Using the 1995 Mw = 8.0 Jalisco-Colima, Mexico, subduction zone earthquake and associated measurements from a nearby GPS array as an example, FEM-generated synthetic Green's functions are combined with standard linear inverse methods to estimate dislocation distributions along the subduction interface. Loading a forward HIPSHS model with dislocation distributions, estimated from FEMs that sequentially relax the HIPSHS assumptions, yields the sensitivity of predicted displacements to each of the HIPSHS assumptions. For the subduction zone models tested and the specific field situation considered, sensitivities to the individual Poisson-solid, isotropy, and homogeneity assumptions can be substantially greater than GPS. measurement uncertainties. Forward modeling quantifies stress coupling between the Mw = 8.0 earthquake and a nearby Mw = 6.3 earthquake that occurred 63 days later. Coulomb stress changes predicted from static HIPSHS models cannot account for the 63-day lag time between events. Alternatively, an FEM that includes a poroelastic oceanic crust, which allows for postseismic pore fluid pressure recovery, can account for the lag time. The pore fluid pressure recovery rate puts an upper limit of 10-17 m2 on the bulk permeability of the oceanic crust. Copyright 2003 by the American Geophysical Union.

Concurrent topological design of composite structures and materials containing multiple phases of distinct Poisson's ratios

NASA Astrophysics Data System (ADS)

Long, Kai; Yuan, Philip F.; Xu, Shanqing; Xie, Yi Min

2018-04-01

Most studies on composites assume that the constituent phases have different values of stiffness. Little attention has been paid to the effect of constituent phases having distinct Poisson's ratios. This research focuses on a concurrent optimization method for simultaneously designing composite structures and materials with distinct Poisson's ratios. The proposed method aims to minimize the mean compliance of the macrostructure with a given mass of base materials. In contrast to the traditional interpolation of the stiffness matrix through numerical results, an interpolation scheme of the Young's modulus and Poisson's ratio using different parameters is adopted. The numerical results demonstrate that the Poisson effect plays a key role in reducing the mean compliance of the final design. An important contribution of the present study is that the proposed concurrent optimization method can automatically distribute base materials with distinct Poisson's ratios between the macrostructural and microstructural levels under a single constraint of the total mass.

Intertime jump statistics of state-dependent Poisson processes.

PubMed

Daly, Edoardo; Porporato, Amilcare

2007-01-01

A method to obtain the probability distribution of the interarrival times of jump occurrences in systems driven by state-dependent Poisson noise is proposed. Such a method uses the survivor function obtained by a modified version of the master equation associated to the stochastic process under analysis. A model for the timing of human activities shows the capability of state-dependent Poisson noise to generate power-law distributions. The application of the method to a model for neuron dynamics and to a hydrological model accounting for land-atmosphere interaction elucidates the origin of characteristic recurrence intervals and possible persistence in state-dependent Poisson models.

Efficient evaluation of the Coulomb force in the Gaussian and finite-element Coulomb method.

PubMed

Kurashige, Yuki; Nakajima, Takahito; Sato, Takeshi; Hirao, Kimihiko

2010-06-28

We propose an efficient method for evaluating the Coulomb force in the Gaussian and finite-element Coulomb (GFC) method, which is a linear-scaling approach for evaluating the Coulomb matrix and energy in large molecular systems. The efficient evaluation of the analytical gradient in the GFC is not straightforward as well as the evaluation of the energy because the SCF procedure with the Coulomb matrix does not give a variational solution for the Coulomb energy. Thus, an efficient approximate method is alternatively proposed, in which the Coulomb potential is expanded in the Gaussian and finite-element auxiliary functions as done in the GFC. To minimize the error in the gradient not just in the energy, the derived functions of the original auxiliary functions of the GFC are used additionally for the evaluation of the Coulomb gradient. In fact, the use of the derived functions significantly improves the accuracy of this approach. Although these additional auxiliary functions enlarge the size of the discretized Poisson equation and thereby increase the computational cost, it maintains the near linear scaling as the GFC and does not affects the overall efficiency of the GFC approach.

Method for resonant measurement

DOEpatents

Rhodes, George W.; Migliori, Albert; Dixon, Raymond D.

1996-01-01

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

Morphology and linear-elastic moduli of random network solids.

PubMed

Nachtrab, Susan; Kapfer, Sebastian C; Arns, Christoph H; Madadi, Mahyar; Mecke, Klaus; Schröder-Turk, Gerd E

2011-06-17

The effective linear-elastic moduli of disordered network solids are analyzed by voxel-based finite element calculations. We analyze network solids given by Poisson-Voronoi processes and by the structure of collagen fiber networks imaged by confocal microscopy. The solid volume fraction ϕ is varied by adjusting the fiber radius, while keeping the structural mesh or pore size of the underlying network fixed. For intermediate ϕ, the bulk and shear modulus are approximated by empirical power-laws K(phi)proptophin and G(phi)proptophim with n≈1.4 and m≈1.7. The exponents for the collagen and the Poisson-Voronoi network solids are similar, and are close to the values n=1.22 and m=2.11 found in a previous voxel-based finite element study of Poisson-Voronoi systems with different boundary conditions. However, the exponents of these empirical power-laws are at odds with the analytic values of n=1 and m=2, valid for low-density cellular structures in the limit of thin beams. We propose a functional form for K(ϕ) that models the cross-over from a power-law at low densities to a porous solid at high densities; a fit of the data to this functional form yields the asymptotic exponent n≈1.00, as expected. Further, both the intensity of the Poisson-Voronoi process and the collagen concentration in the samples, both of which alter the typical pore or mesh size, affect the effective moduli only by the resulting change of the solid volume fraction. These findings suggest that a network solid with the structure of the collagen networks can be modeled in quantitative agreement by a Poisson-Voronoi process. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

NASA Astrophysics Data System (ADS)

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

2010-06-01

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

The transverse Poisson's ratio of composites.

NASA Technical Reports Server (NTRS)

Foye, R. L.

1972-01-01

An expression is developed that makes possible the prediction of Poisson's ratio for unidirectional composites with reference to any pair of orthogonal axes that are normal to the direction of the reinforcing fibers. This prediction appears to be a reasonable one in that it follows the trends of the finite element analysis and the bounding estimates, and has the correct limiting value for zero fiber content. It can only be expected to apply to composites containing stiff, circular, isotropic fibers bonded to a soft matrix material.

Estimation of the engineering elastic constants of a directionally solidified superalloy for finite element structural analysis

NASA Technical Reports Server (NTRS)

Abdul-Aziz, Ali; Kalluri, Sreeramesh

1991-01-01

The temperature-dependent engineering elastic constants of a directionally solidified nickel-base superalloy were estimated from the single-crystal elastic constants of nickel and MAR-MOO2 superalloy by using Wells' method. In this method, the directionally solidified (columnar-grained) nickel-base superalloy was modeled as a transversely isotropic material, and the five independent elastic constants of the transversely isotropic material were determined from the three independent elastic constants of a cubic single crystal. Solidification for both the single crystals and the directionally solidified superalloy was assumed to be along the (001) direction. Temperature-dependent Young's moduli in longitudinal and transverse directions, shear moduli, and Poisson's ratios were tabulated for the directionally solidified nickel-base superalloy. These engineering elastic constants could be used as input for performing finite element structural analysis of directionally solidified turbine engine components.

A new method for constructing analytic elements for groundwater flow.

NASA Astrophysics Data System (ADS)

Strack, O. D.

2007-12-01

The analytic element method is based upon the superposition of analytic functions that are defined throughout the infinite domain, and can be used to meet a variety of boundary conditions. Analytic elements have been use successfully for a number of problems, mainly dealing with the Poisson equation (see, e.g., Theory and Applications of the Analytic Element Method, Reviews of Geophysics, 41,2/1005 2003 by O.D.L. Strack). The majority of these analytic elements consists of functions that exhibit jumps along lines or curves. Such linear analytic elements have been developed also for other partial differential equations, e.g., the modified Helmholz equation and the heat equation, and were constructed by integrating elementary solutions, the point sink and the point doublet, along a line. This approach is limiting for two reasons. First, the existence is required of the elementary solutions, and, second, the integration tends to limit the range of solutions that can be obtained. We present a procedure for generating analytic elements that requires merely the existence of a harmonic function with the desired properties; such functions exist in abundance. The procedure to be presented is used to generalize this harmonic function in such a way that the resulting expression satisfies the applicable differential equation. The approach will be applied, along with numerical examples, for the modified Helmholz equation and for the heat equation, while it is noted that the method is in no way restricted to these equations. The procedure is carried out entirely in terms of complex variables, using Wirtinger calculus.

Poisson-Nernst-Planck Equations for Simulating Biomolecular Diffusion-Reaction Processes II: Size Effects on Ionic Distributions and Diffusion-Reaction Rates

PubMed Central

Lu, Benzhuo; Zhou, Y.C.

2011-01-01

The effects of finite particle size on electrostatics, density profiles, and diffusion have been a long existing topic in the study of ionic solution. The previous size-modified Poisson-Boltzmann and Poisson-Nernst-Planck models are revisited in this article. In contrast to many previous works that can only treat particle species with a single uniform size or two sizes, we generalize the Borukhov model to obtain a size-modified Poisson-Nernst-Planck (SMPNP) model that is able to treat nonuniform particle sizes. The numerical tractability of the model is demonstrated as well. The main contributions of this study are as follows. 1), We show that an (arbitrarily) size-modified PB model is indeed implied by the SMPNP equations under certain boundary/interface conditions, and can be reproduced through numerical solutions of the SMPNP. 2), The size effects in the SMPNP effectively reduce the densities of highly concentrated counterions around the biomolecule. 3), The SMPNP is applied to the diffusion-reaction process for the first time, to our knowledge. In the case of low substrate density near the enzyme reactive site, it is observed that the rate coefficients predicted by SMPNP model are considerably larger than those by the PNP model, suggesting both ions and substrates are subject to finite size effects. 4), An accurate finite element method and a convergent Gummel iteration are developed for the numerical solution of the completely coupled nonlinear system of SMPNP equations. PMID:21575582

Understanding poisson regression.

PubMed

Hayat, Matthew J; Higgins, Melinda

2014-04-01

Nurse investigators often collect study data in the form of counts. Traditional methods of data analysis have historically approached analysis of count data either as if the count data were continuous and normally distributed or with dichotomization of the counts into the categories of occurred or did not occur. These outdated methods for analyzing count data have been replaced with more appropriate statistical methods that make use of the Poisson probability distribution, which is useful for analyzing count data. The purpose of this article is to provide an overview of the Poisson distribution and its use in Poisson regression. Assumption violations for the standard Poisson regression model are addressed with alternative approaches, including addition of an overdispersion parameter or negative binomial regression. An illustrative example is presented with an application from the ENSPIRE study, and regression modeling of comorbidity data is included for illustrative purposes. Copyright 2014, SLACK Incorporated.

Review on solving the forward problem in EEG source analysis

PubMed Central

Hallez, Hans; Vanrumste, Bart; Grech, Roberta; Muscat, Joseph; De Clercq, Wim; Vergult, Anneleen; D'Asseler, Yves; Camilleri, Kenneth P; Fabri, Simon G; Van Huffel, Sabine; Lemahieu, Ignace

2007-01-01

Background The aim of electroencephalogram (EEG) source localization is to find the brain areas responsible for EEG waves of interest. It consists of solving forward and inverse problems. The forward problem is solved by starting from a given electrical source and calculating the potentials at the electrodes. These evaluations are necessary to solve the inverse problem which is defined as finding brain sources which are responsible for the measured potentials at the EEG electrodes. Methods While other reviews give an extensive summary of the both forward and inverse problem, this review article focuses on different aspects of solving the forward problem and it is intended for newcomers in this research field. Results It starts with focusing on the generators of the EEG: the post-synaptic potentials in the apical dendrites of pyramidal neurons. These cells generate an extracellular current which can be modeled by Poisson's differential equation, and Neumann and Dirichlet boundary conditions. The compartments in which these currents flow can be anisotropic (e.g. skull and white matter). In a three-shell spherical head model an analytical expression exists to solve the forward problem. During the last two decades researchers have tried to solve Poisson's equation in a realistically shaped head model obtained from 3D medical images, which requires numerical methods. The following methods are compared with each other: the boundary element method (BEM), the finite element method (FEM) and the finite difference method (FDM). In the last two methods anisotropic conducting compartments can conveniently be introduced. Then the focus will be set on the use of reciprocity in EEG source localization. It is introduced to speed up the forward calculations which are here performed for each electrode position rather than for each dipole position. Solving Poisson's equation utilizing FEM and FDM corresponds to solving a large sparse linear system. Iterative methods are required to solve these sparse linear systems. The following iterative methods are discussed: successive over-relaxation, conjugate gradients method and algebraic multigrid method. Conclusion Solving the forward problem has been well documented in the past decades. In the past simplified spherical head models are used, whereas nowadays a combination of imaging modalities are used to accurately describe the geometry of the head model. Efforts have been done on realistically describing the shape of the head model, as well as the heterogenity of the tissue types and realistically determining the conductivity. However, the determination and validation of the in vivo conductivity values is still an important topic in this field. In addition, more studies have to be done on the influence of all the parameters of the head model and of the numerical techniques on the solution of the forward problem. PMID:18053144

Elastic properties of rigid fiber-reinforced composites

NASA Astrophysics Data System (ADS)

Chen, J.; Thorpe, M. F.; Davis, L. C.

1995-05-01

We study the elastic properties of rigid fiber-reinforced composites with perfect bonding between fibers and matrix, and also with sliding boundary conditions. In the dilute region, there exists an exact analytical solution. Around the rigidity threshold we find the elastic moduli and Poisson's ratio by decomposing the deformation into a compression mode and a rotation mode. For perfect bonding, both modes are important, whereas only the compression mode is operative for sliding boundary conditions. We employ the digital-image-based method and a finite element analysis to perform computer simulations which confirm our analytical predictions.

Analysis of ballistic transport in nanoscale devices by using an accelerated finite element contact block reduction approach

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

Li, H.; Li, G., E-mail: gli@clemson.edu

2014-08-28

An accelerated Finite Element Contact Block Reduction (FECBR) approach is presented for computational analysis of ballistic transport in nanoscale electronic devices with arbitrary geometry and unstructured mesh. Finite element formulation is developed for the theoretical CBR/Poisson model. The FECBR approach is accelerated through eigen-pair reduction, lead mode space projection, and component mode synthesis techniques. The accelerated FECBR is applied to perform quantum mechanical ballistic transport analysis of a DG-MOSFET with taper-shaped extensions and a DG-MOSFET with Si/SiO{sub 2} interface roughness. The computed electrical transport properties of the devices obtained from the accelerated FECBR approach and associated computational cost as amore » function of system degrees of freedom are compared with those obtained from the original CBR and direct inversion methods. The performance of the accelerated FECBR in both its accuracy and efficiency is demonstrated.« less

Modeling of monolayer charge-stabilized colloidal crystals with static hexagonal crystal lattice

NASA Astrophysics Data System (ADS)

Nagatkin, A. N.; Dyshlovenko, P. E.

2018-01-01

The mathematical model of monolayer colloidal crystals of charged hard spheres in liquid electrolyte is proposed. The particles in the monolayer are arranged into the two-dimensional hexagonal crystal lattice. The model enables finding elastic constants of the crystals from the stress-strain dependencies. The model is based on the nonlinear Poisson-Boltzmann differential equation. The Poisson-Boltzmann equation is solved numerically by the finite element method for any spatial configuration. The model has five geometrical and electrical parameters. The model is used to study the crystal with particles comparable in size with the Debye length of the electrolyte. The first- and second-order elastic constants are found for a broad range of densities. The model crystal turns out to be stable relative to small uniform stretching and shearing. It is also demonstrated that the Cauchy relation is not fulfilled in the crystal. This means that the pair effective interaction of any kind is not sufficient to proper model the elasticity of colloids within the one-component approach.

Zero-inflated Poisson model based likelihood ratio test for drug safety signal detection.

PubMed

Huang, Lan; Zheng, Dan; Zalkikar, Jyoti; Tiwari, Ram

2017-02-01

In recent decades, numerous methods have been developed for data mining of large drug safety databases, such as Food and Drug Administration's (FDA's) Adverse Event Reporting System, where data matrices are formed by drugs such as columns and adverse events as rows. Often, a large number of cells in these data matrices have zero cell counts and some of them are "true zeros" indicating that the drug-adverse event pairs cannot occur, and these zero counts are distinguished from the other zero counts that are modeled zero counts and simply indicate that the drug-adverse event pairs have not occurred yet or have not been reported yet. In this paper, a zero-inflated Poisson model based likelihood ratio test method is proposed to identify drug-adverse event pairs that have disproportionately high reporting rates, which are also called signals. The maximum likelihood estimates of the model parameters of zero-inflated Poisson model based likelihood ratio test are obtained using the expectation and maximization algorithm. The zero-inflated Poisson model based likelihood ratio test is also modified to handle the stratified analyses for binary and categorical covariates (e.g. gender and age) in the data. The proposed zero-inflated Poisson model based likelihood ratio test method is shown to asymptotically control the type I error and false discovery rate, and its finite sample performance for signal detection is evaluated through a simulation study. The simulation results show that the zero-inflated Poisson model based likelihood ratio test method performs similar to Poisson model based likelihood ratio test method when the estimated percentage of true zeros in the database is small. Both the zero-inflated Poisson model based likelihood ratio test and likelihood ratio test methods are applied to six selected drugs, from the 2006 to 2011 Adverse Event Reporting System database, with varying percentages of observed zero-count cells.

CFD-ACE+: a CAD system for simulation and modeling of MEMS

NASA Astrophysics Data System (ADS)

Stout, Phillip J.; Yang, H. Q.; Dionne, Paul; Leonard, Andy; Tan, Zhiqiang; Przekwas, Andrzej J.; Krishnan, Anantha

1999-03-01

Computer aided design (CAD) systems are a key to designing and manufacturing MEMS with higher performance/reliability, reduced costs, shorter prototyping cycles and improved time- to-market. One such system is CFD-ACE+MEMS, a modeling and simulation environment for MEMS which includes grid generation, data visualization, graphical problem setup, and coupled fluidic, thermal, mechanical, electrostatic, and magnetic physical models. The fluid model is a 3D multi- block, structured/unstructured/hybrid, pressure-based, implicit Navier-Stokes code with capabilities for multi- component diffusion, multi-species transport, multi-step gas phase chemical reactions, surface reactions, and multi-media conjugate heat transfer. The thermal model solves the total enthalpy from of the energy equation. The energy equation includes unsteady, convective, conductive, species energy, viscous dissipation, work, and radiation terms. The electrostatic model solves Poisson's equation. Both the finite volume method and the boundary element method (BEM) are available for solving Poisson's equation. The BEM method is useful for unbounded problems. The magnetic model solves for the vector magnetic potential from Maxwell's equations including eddy currents but neglecting displacement currents. The mechanical model is a finite element stress/deformation solver which has been coupled to the flow, heat, electrostatic, and magnetic calculations to study flow, thermal electrostatically, and magnetically included deformations of structures. The mechanical or structural model can accommodate elastic and plastic materials, can handle large non-linear displacements, and can model isotropic and anisotropic materials. The thermal- mechanical coupling involves the solution of the steady state Navier equation with thermoelastic deformation. The electrostatic-mechanical coupling is a calculation of the pressure force due to surface charge on the mechanical structure. Results of CFD-ACE+MEMS modeling of MEMS such as cantilever beams, accelerometers, and comb drives are discussed.

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.

A Galerkin formulation of the MIB method for three dimensional elliptic interface problems

PubMed Central

Xia, Kelin; Wei, Guo-Wei

2014-01-01

We develop a three dimensional (3D) Galerkin formulation of the matched interface and boundary (MIB) method for solving elliptic partial differential equations (PDEs) with discontinuous coefficients, i.e., the elliptic interface problem. The present approach builds up two sets of elements respectively on two extended subdomains which both include the interface. As a result, two sets of elements overlap each other near the interface. Fictitious solutions are defined on the overlapping part of the elements, so that the differentiation operations of the original PDEs can be discretized as if there was no interface. The extra coefficients of polynomial basis functions, which furnish the overlapping elements and solve the fictitious solutions, are determined by interface jump conditions. Consequently, the interface jump conditions are rigorously enforced on the interface. The present method utilizes Cartesian meshes to avoid the mesh generation in conventional finite element methods (FEMs). We implement the proposed MIB Galerkin method with three different elements, namely, rectangular prism element, five-tetrahedron element and six-tetrahedron element, which tile the Cartesian mesh without introducing any new node. The accuracy, stability and robustness of the proposed 3D MIB Galerkin are extensively validated over three types of elliptic interface problems. In the first type, interfaces are analytically defined by level set functions. These interfaces are relatively simple but admit geometric singularities. In the second type, interfaces are defined by protein surfaces, which are truly arbitrarily complex. The last type of interfaces originates from multiprotein complexes, such as molecular motors. Near second order accuracy has been confirmed for all of these problems. To our knowledge, it is the first time for an FEM to show a near second order convergence in solving the Poisson equation with realistic protein surfaces. Additionally, the present work offers the first known near second order accurate method for C1 continuous or H2 continuous solutions associated with a Lipschitz continuous interface in a 3D setting. PMID:25309038

MPSalsa Version 1.5: A Finite Element Computer Program for Reacting Flow Problems: Part 1 - Theoretical Development

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

Devine, K.D.; Hennigan, G.L.; Hutchinson, S.A.

1999-01-01

The theoretical background for the finite element computer program, MPSalsa Version 1.5, is presented in detail. MPSalsa is designed to solve laminar or turbulent low Mach number, two- or three-dimensional incompressible and variable density reacting fluid flows on massively parallel computers, using a Petrov-Galerkin finite element formulation. The code has the capability to solve coupled fluid flow (with auxiliary turbulence equations), heat transport, multicomponent species transport, and finite-rate chemical reactions, and to solve coupled multiple Poisson or advection-diffusion-reaction equations. The program employs the CHEMKIN library to provide a rigorous treatment of multicomponent ideal gas kinetics and transport. Chemical reactions occurringmore » in the gas phase and on surfaces are treated by calls to CHEMKIN and SURFACE CHEMK3N, respectively. The code employs unstructured meshes, using the EXODUS II finite element database suite of programs for its input and output files. MPSalsa solves both transient and steady flows by using fully implicit time integration, an inexact Newton method and iterative solvers based on preconditioned Krylov methods as implemented in the Aztec. solver library.« less

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.

Poisson's Ratio and Auxetic Properties of Natural Rocks

NASA Astrophysics Data System (ADS)

Ji, Shaocheng; Li, Le; Motra, Hem Bahadur; Wuttke, Frank; Sun, Shengsi; Michibayashi, Katsuyoshi; Salisbury, Matthew H.

2018-02-01

Here we provide an appraisal of the Poisson's ratios (υ) for natural elements, common oxides, silicate minerals, and rocks with the purpose of searching for naturally auxetic materials. The Poisson's ratios of equivalently isotropic polycrystalline aggregates were calculated from dynamically measured elastic properties. Alpha-cristobalite is currently the only known naturally occurring mineral that has exclusively negative υ values at 20-1,500°C. Quartz and potentially berlinite (AlPO4) display auxetic behavior in the vicinity of their α-β structure transition. None of the crystalline igneous and metamorphic rocks (e.g., amphibolite, gabbro, granite, peridotite, and schist) display auxetic behavior at pressures of >5 MPa and room temperature. Our experimental measurements showed that quartz-rich sedimentary rocks (i.e., sandstone and siltstone) are most likely to be the only rocks with negative Poisson's ratios at low confining pressures (≤200 MPa) because their main constituent mineral, α-quartz, already has extremely low Poisson's ratio (υ = 0.08) and they contain microcracks, micropores, and secondary minerals. This finding may provide a new explanation for formation of dome-and-basin structures in quartz-rich sedimentary rocks in response to a horizontal compressional stress in the upper crust.

Stiffness and Poisson ratio in longitudinal compression of fiber yarns in meso-FE modelling of composite reinforcement forming

NASA Astrophysics Data System (ADS)

Wang, D.; Naouar, N.; Vidal-Salle, E.; Boisse, P.

2018-05-01

In meso-scale finite element modeling, the yarns of the reinforcement are considered to be solids made of a continuous material in contact with their neighbors. The present paper consider the mechanical behavior of these yarns that can happen for some loadings of the reinforcement. The yarns present a specific mechanical behavior when under longitudinal compression because they are made up of a large number of fibers, Local buckling of the fibers causes the compressive stiffness of the continuous material representing the yarn to be much weaker than when under tension. In addition, longitudinal compression causes an important transverse expansion. It is shown that the transverse expansion can be depicted by a Poisson ratio that remained roughly constant when the yarn length and the compression strain varied. Buckling of the fibers significantly increases the transverse dimensions of the yarn which leads to a large Poisson ratio (up to 12 for a yarn analyzed in the present study). Meso-scale finite element simulations of reinforcements with binder yarns submitted to longitudinal compression showed that these improvements led to results in good agreement with micro-CT analyses.

Nonlocal Poisson-Fermi double-layer models: Effects of nonuniform ion sizes on double-layer structure

NASA Astrophysics Data System (ADS)

Xie, Dexuan; Jiang, Yi

2018-05-01

This paper reports a nonuniform ionic size nonlocal Poisson-Fermi double-layer model (nuNPF) and a uniform ionic size nonlocal Poisson-Fermi double-layer model (uNPF) for an electrolyte mixture of multiple ionic species, variable voltages on electrodes, and variable induced charges on boundary segments. The finite element solvers of nuNPF and uNPF are developed and applied to typical double-layer tests defined on a rectangular box, a hollow sphere, and a hollow rectangle with a charged post. Numerical results show that nuNPF can significantly improve the quality of the ionic concentrations and electric fields generated from uNPF, implying that the effect of nonuniform ion sizes is a key consideration in modeling the double-layer structure.

Symmetries of hyper-Kähler (or Poisson gauge field) hierarchy

NASA Astrophysics Data System (ADS)

Takasaki, K.

1990-08-01

Symmetry properties of the space of complex (or formal) hyper-Kähler metrics are studied in the language of hyper-Kähler hierarchies. The construction of finite symmetries is analogous to the theory of Riemann-Hilbert transformations, loop group elements now taking values in a (pseudo-) group of canonical transformations of a simplectic manifold. In spite of their highly nonlinear and involved nature, infinitesimal expressions of these symmetries are shown to have a rather simple form. These infinitesimal transformations are extended to the Plebanski key functions to give rise to a nonlinear realization of a Poisson loop algebra. The Poisson algebra structure turns out to originate in a contact structure behind a set of symplectic structures inherent in the hyper-Kähler hierarchy. Possible relations to membrane theory are briefly discussed.

Prediction of high temperature metal matrix composite ply properties

NASA Technical Reports Server (NTRS)

Caruso, J. J.; Chamis, C. C.

1988-01-01

The application of the finite element method (superelement technique) in conjunction with basic concepts from mechanics of materials theory is demonstrated to predict the thermomechanical behavior of high temperature metal matrix composites (HTMMC). The simulated behavior is used as a basis to establish characteristic properties of a unidirectional composite idealized an as equivalent homogeneous material. The ply properties predicted include: thermal properties (thermal conductivities and thermal expansion coefficients) and mechanical properties (moduli and Poisson's ratio). These properties are compared with those predicted by a simplified, analytical composite micromechanics model. The predictive capabilities of the finite element method and the simplified model are illustrated through the simulation of the thermomechanical behavior of a P100-graphite/copper unidirectional composite at room temperature and near matrix melting temperature. The advantage of the finite element analysis approach is its ability to more precisely represent the composite local geometry and hence capture the subtle effects that are dependent on this. The closed form micromechanics model does a good job at representing the average behavior of the constituents to predict composite behavior.

A new finite element and finite difference hybrid method for computing electrostatics of ionic solvated biomolecule

NASA Astrophysics Data System (ADS)

Ying, Jinyong; Xie, Dexuan

2015-10-01

The Poisson-Boltzmann equation (PBE) is one widely-used implicit solvent continuum model for calculating electrostatics of ionic solvated biomolecule. In this paper, a new finite element and finite difference hybrid method is presented to solve PBE efficiently based on a special seven-overlapped box partition with one central box containing the solute region and surrounded by six neighboring boxes. In particular, an efficient finite element solver is applied to the central box while a fast preconditioned conjugate gradient method using a multigrid V-cycle preconditioning is constructed for solving a system of finite difference equations defined on a uniform mesh of each neighboring box. Moreover, the PBE domain, the box partition, and an interface fitted tetrahedral mesh of the central box can be generated adaptively for a given PQR file of a biomolecule. This new hybrid PBE solver is programmed in C, Fortran, and Python as a software tool for predicting electrostatics of a biomolecule in a symmetric 1:1 ionic solvent. Numerical results on two test models with analytical solutions and 12 proteins validate this new software tool, and demonstrate its high performance in terms of CPU time and memory usage.

A New Axi-Symmetric Element for Thin Walled Structures

NASA Astrophysics Data System (ADS)

Cardoso, Rui P. R.; Yoon, Jeong Whan; Dick, Robert E.

2010-06-01

A new axi-symmetric finite element for sheet metal forming applications is presented in this work. It uses the solid-shell element's concept with only a single element layer and multiple integration points along the thickness direction. The cross section of the element is composed of four nodes with two degrees of freedom each. The proposed formulation overcomes major locking pathologies including transverse shear locking, Poisson's locking and volumetric locking. Some examples are shown to demonstrate the performance and accuracy of the proposed element with special focus on the numerical simulations for the beverage can industry.

A rigorous solution of the Navier-Stokes equations for unsteady viscous flow at high Reynolds numbers around oscillating airfoils

NASA Technical Reports Server (NTRS)

Bratanow, T.; Aksu, H.; Spehert, T.

1975-01-01

A method based on the Navier-Stokes equations was developed for analyzing the unsteady incompressible viscous flow around oscillating airfoils at high Reynolds numbers. The Navier-Stokes equations have been integrated in their classical Helmholtz vorticity transport equation form, and the instantaneous velocity field at each time step was determined by the solution of Poisson's equation. A refined finite element was utilized to allow for a conformable solution of the stream function and its first space derivatives at the element interfaces. A corresponding set of accurate boundary conditions was applied; thus obtaining a rigorous solution for the velocity field. The details of the computational procedure and examples of computed results describing the unsteady flow characteristics around the airfoil are presented.

Generation of Non-Homogeneous Poisson Processes by Thinning: Programming Considerations and Comparision with Competing Algorithms.

DTIC Science & Technology

1978-12-01

Poisson processes . The method is valid for Poisson processes with any given intensity function. The basic thinning algorithm is modified to exploit several refinements which reduce computer execution time by approximately one-third. The basic and modified thinning programs are compared with the Poisson decomposition and gap-statistics algorithm, which is easily implemented for Poisson processes with intensity functions of the form exp(a sub 0 + a sub 1t + a sub 2 t-squared. The thinning programs are competitive in both execution

Numerical calibration of the stable poisson loaded specimen

NASA Technical Reports Server (NTRS)

Ghosn, Louis J.; Calomino, Anthony M.; Brewer, Dave N.

1992-01-01

An analytical calibration of the Stable Poisson Loaded (SPL) specimen is presented. The specimen configuration is similar to the ASTM E-561 compact-tension specimen with displacement controlled wedge loading used for R-Curve determination. The crack mouth opening displacements (CMOD's) are produced by the diametral expansion of an axially compressed cylindrical pin located in the wake of a machined notch. Due to the unusual loading configuration, a three-dimensional finite element analysis was performed with gap elements simulating the contact between the pin and specimen. In this report, stress intensity factors, CMOD's, and crack displacement profiles are reported for different crack lengths and different contacting conditions. It was concluded that the computed stress intensity factor decreases sharply with increasing crack length, thus making the SPL specimen configuration attractive for fracture testing of brittle, high modulus materials.

Analytical stress intensity solution for the Stable Poisson Loaded specimen

NASA Technical Reports Server (NTRS)

Ghosn, Louis J.; Calomino, Anthony M.; Brewer, David N.

1993-01-01

An analytical calibration of the Stable Poisson Loaded (SPL) specimen is presented. The specimen configuration is similar to the ASTM E-561 compact-tension specimen with displacement controlled wedge loading used for R-curve determination. The crack mouth opening displacements (CMODs) are produced by the diametral expansion of an axially compressed cylindrical pin located in the wake of a machined notch. Due to the unusual loading configuration, a three-dimensional finite element analysis was performed with gap elements simulating the contact between the pin and specimen. In this report, stress intensity factors, CMODs, and crack displacement profiles, are reported for different crack lengths and different contacting conditions. It was concluded that the computed stress intensity factor decreases sharply with increasing crack length thus making the SPL specimen configuration attractive for fracture testing of brittle, high modulus materials.

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

Pratap, Surender; Sarkar, Niladri, E-mail: niladri@pilani.bits-pilani.ac.in

Self-Consistent Quantum Method using Schrodinger-Poisson equations have been used for determining the Channel electron density of Nano-Scale MOSFETs for 6nm and 9nm thick channels. The 6nm thick MOSFET show the peak of the electron density at the middle where as the 9nm thick MOSFET shows the accumulation of the electrons at the oxide/semiconductor interface. The electron density in the channel is obtained from the diagonal elements of the density matrix; [ρ]=[1/(1+exp(β(H − μ)))] A Tridiagonal Hamiltonian Matrix [H] is constructed for the oxide/channel/oxide 1D structure for the dual gate MOSFET. This structure is discretized and Finite-Difference method is used formore » constructing the matrix equation. The comparison of these results which are obtained by Quantum methods are done with Semi-Classical methods.« less

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

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.

Poisson denoising on the sphere

NASA Astrophysics Data System (ADS)

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

2009-08-01

In the scope of the Fermi mission, Poisson noise removal should improve data quality and make source detection easier. This paper presents a method for Poisson data denoising on sphere, called Multi-Scale Variance Stabilizing Transform on Sphere (MS-VSTS). This method is based on a Variance Stabilizing Transform (VST), a transform which aims to stabilize a Poisson data set such that each stabilized sample has an (asymptotically) constant variance. In addition, for the VST used in the method, the transformed data are asymptotically Gaussian. Thus, MS-VSTS consists in decomposing the data into a sparse multi-scale dictionary (wavelets, curvelets, ridgelets...), and then applying a VST on the coefficients in order to get quasi-Gaussian stabilized coefficients. In this present article, the used multi-scale transform is the Isotropic Undecimated Wavelet Transform. Then, hypothesis tests are made to detect significant coefficients, and the denoised image is reconstructed with an iterative method based on Hybrid Steepest Descent (HST). The method is tested on simulated Fermi data.

The application of signal detection theory to optics

NASA Technical Reports Server (NTRS)

Helstrom, C. W.

1971-01-01

The restoration of images focused on a photosensitive surface is treated from the standpoint of maximum likelihood estimation, taking into account the Poisson distributions of the observed data, which are the numbers of photoelectrons from various elements of the surface. A detector of an image focused on such a surface utilizes a certain linear combination of those numbers as the optimum detection statistic. Methods for calculating the false alarm and detection probabilities are proposed. It is shown that measuring noncommuting observables in an ideal quantum receiver cannot yield a lower Bayes cost than that attainable by a system measuring only commuting observables.

A coarse-grid projection method for accelerating incompressible flow computations

NASA Astrophysics Data System (ADS)

San, Omer; Staples, Anne

2011-11-01

We present a coarse-grid projection (CGP) algorithm for accelerating incompressible flow computations, which is applicable to methods involving Poisson equations as incompressibility constraints. CGP methodology is a modular approach that facilitates data transfer with simple interpolations and uses black-box solvers for the Poisson and advection-diffusion equations in the flow solver. Here, we investigate a particular CGP method for the vorticity-stream function formulation that uses the full weighting operation for mapping from fine to coarse grids, the third-order Runge-Kutta method for time stepping, and finite differences for the spatial discretization. After solving the Poisson equation on a coarsened grid, bilinear interpolation is used to obtain the fine data for consequent time stepping on the full grid. We compute several benchmark flows: the Taylor-Green vortex, a vortex pair merging, a double shear layer, decaying turbulence and the Taylor-Green vortex on a distorted grid. In all cases we use either FFT-based or V-cycle multigrid linear-cost Poisson solvers. Reducing the number of degrees of freedom of the Poisson solver by powers of two accelerates these computations while, for the first level of coarsening, retaining the same level of accuracy in the fine resolution vorticity field.

A meta-model analysis of a finite element simulation for defining poroelastic properties of intervertebral discs.

PubMed

Nikkhoo, Mohammad; Hsu, Yu-Chun; Haghpanahi, Mohammad; Parnianpour, Mohamad; Wang, Jaw-Lin

2013-06-01

Finite element analysis is an effective tool to evaluate the material properties of living tissue. For an interactive optimization procedure, the finite element analysis usually needs many simulations to reach a reasonable solution. The meta-model analysis of finite element simulation can be used to reduce the computation of a structure with complex geometry or a material with composite constitutive equations. The intervertebral disc is a complex, heterogeneous, and hydrated porous structure. A poroelastic finite element model can be used to observe the fluid transferring, pressure deviation, and other properties within the disc. Defining reasonable poroelastic material properties of the anulus fibrosus and nucleus pulposus is critical for the quality of the simulation. We developed a material property updating protocol, which is basically a fitting algorithm consisted of finite element simulations and a quadratic response surface regression. This protocol was used to find the material properties, such as the hydraulic permeability, elastic modulus, and Poisson's ratio, of intact and degenerated porcine discs. The results showed that the in vitro disc experimental deformations were well fitted with limited finite element simulations and a quadratic response surface regression. The comparison of material properties of intact and degenerated discs showed that the hydraulic permeability significantly decreased but Poisson's ratio significantly increased for the degenerated discs. This study shows that the developed protocol is efficient and effective in defining material properties of a complex structure such as the intervertebral disc.

Noise parameter estimation for poisson corrupted images using variance stabilization transforms.

PubMed

Jin, Xiaodan; Xu, Zhenyu; Hirakawa, Keigo

2014-03-01

Noise is present in all images captured by real-world image sensors. Poisson distribution is said to model the stochastic nature of the photon arrival process and agrees with the distribution of measured pixel values. We propose a method for estimating unknown noise parameters from Poisson corrupted images using properties of variance stabilization. With a significantly lower computational complexity and improved stability, the proposed estimation technique yields noise parameters that are comparable in accuracy to the state-of-art methods.

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.

Exact solution for the Poisson field in a semi-infinite strip.

PubMed

Cohen, Yossi; Rothman, Daniel H

2017-04-01

The Poisson equation is associated with many physical processes. Yet exact analytic solutions for the two-dimensional Poisson field are scarce. Here we derive an analytic solution for the Poisson equation with constant forcing in a semi-infinite strip. We provide a method that can be used to solve the field in other intricate geometries. We show that the Poisson flux reveals an inverse square-root singularity at a tip of a slit, and identify a characteristic length scale in which a small perturbation, in a form of a new slit, is screened by the field. We suggest that this length scale expresses itself as a characteristic spacing between tips in real Poisson networks that grow in response to fluxes at tips.

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.

New solution decomposition and minimization schemes for Poisson-Boltzmann equation in calculation of biomolecular electrostatics

NASA Astrophysics Data System (ADS)

Xie, Dexuan

2014-10-01

The Poisson-Boltzmann equation (PBE) is one widely-used implicit solvent continuum model in the calculation of electrostatic potential energy for biomolecules in ionic solvent, but its numerical solution remains a challenge due to its strong singularity and nonlinearity caused by its singular distribution source terms and exponential nonlinear terms. To effectively deal with such a challenge, in this paper, new solution decomposition and minimization schemes are proposed, together with a new PBE analysis on solution existence and uniqueness. Moreover, a PBE finite element program package is developed in Python based on the FEniCS program library and GAMer, a molecular surface and volumetric mesh generation program package. Numerical tests on proteins and a nonlinear Born ball model with an analytical solution validate the new solution decomposition and minimization schemes, and demonstrate the effectiveness and efficiency of the new PBE finite element program package.

Toward negative Poisson's ratio composites: Investigation of the auxetic behavior of fibrous networks

NASA Astrophysics Data System (ADS)

Tatlier, Mehmet Seha

Random fibrous can be found among natural and synthetic materials. Some of these random fibrous networks possess negative Poisson's ratio and they are extensively called auxetic materials. The governing mechanisms behind this counter intuitive property in random networks are yet to be understood and this kind of auxetic material remains widely under-explored. However, most of synthetic auxetic materials suffer from their low strength. This shortcoming can be rectified by developing high strength auxetic composites. The process of embedding auxetic random fibrous networks in a polymer matrix is an attractive alternate route to the manufacture of auxetic composites, however before such an approach can be developed, a methodology for designing fibrous networks with the desired negative Poisson's ratios must first be established. This requires an understanding of the factors which bring about negative Poisson's ratios in these materials. In this study, a numerical model is presented in order to investigate the auxetic behavior in compressed random fiber networks. Finite element analyses of three-dimensional stochastic fiber networks were performed to gain insight into the effects of parameters such as network anisotropy, network density, and degree of network compression on the out-of-plane Poisson's ratio and Young's modulus. The simulation results suggest that the compression is the critical parameter that gives rise to negative Poisson's ratio while anisotropy significantly promotes the auxetic behavior. This model can be utilized to design fibrous auxetic materials and to evaluate feasibility of developing auxetic composites by using auxetic fibrous networks as the reinforcing layer.

A Conway-Maxwell-Poisson (CMP) model to address data dispersion on positron emission tomography.

PubMed

Santarelli, Maria Filomena; Della Latta, Daniele; Scipioni, Michele; Positano, Vincenzo; Landini, Luigi

2016-10-01

Positron emission tomography (PET) in medicine exploits the properties of positron-emitting unstable nuclei. The pairs of γ- rays emitted after annihilation are revealed by coincidence detectors and stored as projections in a sinogram. It is well known that radioactive decay follows a Poisson distribution; however, deviation from Poisson statistics occurs on PET projection data prior to reconstruction due to physical effects, measurement errors, correction of deadtime, scatter, and random coincidences. A model that describes the statistical behavior of measured and corrected PET data can aid in understanding the statistical nature of the data: it is a prerequisite to develop efficient reconstruction and processing methods and to reduce noise. The deviation from Poisson statistics in PET data could be described by the Conway-Maxwell-Poisson (CMP) distribution model, which is characterized by the centring parameter λ and the dispersion parameter ν, the latter quantifying the deviation from a Poisson distribution model. In particular, the parameter ν allows quantifying over-dispersion (ν<1) or under-dispersion (ν>1) of data. A simple and efficient method for λ and ν parameters estimation is introduced and assessed using Monte Carlo simulation for a wide range of activity values. The application of the method to simulated and experimental PET phantom data demonstrated that the CMP distribution parameters could detect deviation from the Poisson distribution both in raw and corrected PET data. It may be usefully implemented in image reconstruction algorithms and quantitative PET data analysis, especially in low counting emission data, as in dynamic PET data, where the method demonstrated the best accuracy. Copyright © 2016 Elsevier Ltd. 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.

Low Dose PET Image Reconstruction with Total Variation Using Alternating Direction Method.

PubMed

Yu, Xingjian; Wang, Chenye; Hu, Hongjie; Liu, Huafeng

2016-01-01

In this paper, a total variation (TV) minimization strategy is proposed to overcome the problem of sparse spatial resolution and large amounts of noise in low dose positron emission tomography (PET) imaging reconstruction. Two types of objective function were established based on two statistical models of measured PET data, least-square (LS) TV for the Gaussian distribution and Poisson-TV for the Poisson distribution. To efficiently obtain high quality reconstructed images, the alternating direction method (ADM) is used to solve these objective functions. As compared with the iterative shrinkage/thresholding (IST) based algorithms, the proposed ADM can make full use of the TV constraint and its convergence rate is faster. The performance of the proposed approach is validated through comparisons with the expectation-maximization (EM) method using synthetic and experimental biological data. In the comparisons, the results of both LS-TV and Poisson-TV are taken into consideration to find which models are more suitable for PET imaging, in particular low-dose PET. To evaluate the results quantitatively, we computed bias, variance, and the contrast recovery coefficient (CRC) and drew profiles of the reconstructed images produced by the different methods. The results show that both Poisson-TV and LS-TV can provide a high visual quality at a low dose level. The bias and variance of the proposed LS-TV and Poisson-TV methods are 20% to 74% less at all counting levels than those of the EM method. Poisson-TV gives the best performance in terms of high-accuracy reconstruction with the lowest bias and variance as compared to the ground truth (14.3% less bias and 21.9% less variance). In contrast, LS-TV gives the best performance in terms of the high contrast of the reconstruction with the highest CRC.

Low Dose PET Image Reconstruction with Total Variation Using Alternating Direction Method

PubMed Central

Yu, Xingjian; Wang, Chenye; Hu, Hongjie; Liu, Huafeng

2016-01-01

In this paper, a total variation (TV) minimization strategy is proposed to overcome the problem of sparse spatial resolution and large amounts of noise in low dose positron emission tomography (PET) imaging reconstruction. Two types of objective function were established based on two statistical models of measured PET data, least-square (LS) TV for the Gaussian distribution and Poisson-TV for the Poisson distribution. To efficiently obtain high quality reconstructed images, the alternating direction method (ADM) is used to solve these objective functions. As compared with the iterative shrinkage/thresholding (IST) based algorithms, the proposed ADM can make full use of the TV constraint and its convergence rate is faster. The performance of the proposed approach is validated through comparisons with the expectation-maximization (EM) method using synthetic and experimental biological data. In the comparisons, the results of both LS-TV and Poisson-TV are taken into consideration to find which models are more suitable for PET imaging, in particular low-dose PET. To evaluate the results quantitatively, we computed bias, variance, and the contrast recovery coefficient (CRC) and drew profiles of the reconstructed images produced by the different methods. The results show that both Poisson-TV and LS-TV can provide a high visual quality at a low dose level. The bias and variance of the proposed LS-TV and Poisson-TV methods are 20% to 74% less at all counting levels than those of the EM method. Poisson-TV gives the best performance in terms of high-accuracy reconstruction with the lowest bias and variance as compared to the ground truth (14.3% less bias and 21.9% less variance). In contrast, LS-TV gives the best performance in terms of the high contrast of the reconstruction with the highest CRC. PMID:28005929

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

An intrinsic algorithm for parallel Poisson disk sampling on arbitrary surfaces.

PubMed

Ying, Xiang; Xin, Shi-Qing; Sun, Qian; He, Ying

2013-09-01

Poisson disk sampling has excellent spatial and spectral properties, and plays an important role in a variety of visual computing. Although many promising algorithms have been proposed for multidimensional sampling in euclidean space, very few studies have been reported with regard to the problem of generating Poisson disks on surfaces due to the complicated nature of the surface. This paper presents an intrinsic algorithm for parallel Poisson disk sampling on arbitrary surfaces. In sharp contrast to the conventional parallel approaches, our method neither partitions the given surface into small patches nor uses any spatial data structure to maintain the voids in the sampling domain. Instead, our approach assigns each sample candidate a random and unique priority that is unbiased with regard to the distribution. Hence, multiple threads can process the candidates simultaneously and resolve conflicts by checking the given priority values. Our algorithm guarantees that the generated Poisson disks are uniformly and randomly distributed without bias. It is worth noting that our method is intrinsic and independent of the embedding space. This intrinsic feature allows us to generate Poisson disk patterns on arbitrary surfaces in IR(n). To our knowledge, this is the first intrinsic, parallel, and accurate algorithm for surface Poisson disk sampling. Furthermore, by manipulating the spatially varying density function, we can obtain adaptive sampling easily.

A Finite Element Solution of Lateral Periodic Poisson-Boltzmann Model for Membrane Channel Proteins.

PubMed

Ji, Nan; Liu, Tiantian; Xu, Jingjie; Shen, Longzhu Q; Lu, Benzhuo

2018-02-28

Membrane channel proteins control the diffusion of ions across biological membranes. They are closely related to the processes of various organizational mechanisms, such as: cardiac impulse, muscle contraction and hormone secretion. Introducing a membrane region into implicit solvation models extends the ability of the Poisson-Boltzmann (PB) equation to handle membrane proteins. The use of lateral periodic boundary conditions can properly simulate the discrete distribution of membrane proteins on the membrane plane and avoid boundary effects, which are caused by the finite box size in the traditional PB calculations. In this work, we: (1) develop a first finite element solver (FEPB) to solve the PB equation with a two-dimensional periodicity for membrane channel proteins, with different numerical treatments of the singular charges distributions in the channel protein; (2) add the membrane as a dielectric slab in the PB model, and use an improved mesh construction method to automatically identify the membrane channel/pore region even with a tilt angle relative to the z -axis; and (3) add a non-polar solvation energy term to complete the estimation of the total solvation energy of a membrane protein. A mesh resolution of about 0.25 Å (cubic grid space)/0.36 Å (tetrahedron edge length) is found to be most accurate in linear finite element calculation of the PB solvation energy. Computational studies are performed on a few exemplary molecules. The results indicate that all factors, the membrane thickness, the length of periodic box, membrane dielectric constant, pore region dielectric constant, and ionic strength, have individually considerable influence on the solvation energy of a channel protein. This demonstrates the necessity to treat all of those effects in the PB model for membrane protein simulations.

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.

Direct Density Functional Energy Minimization using an Tetrahedral Finite Element Grid

NASA Astrophysics Data System (ADS)

Vaught, A.; Schmidt, K. E.; Chizmeshya, A. V. G.

1998-03-01

We describe an O(N) (N proportional to volume) technique for solving electronic structure problems using the finite element method (FEM). A real--space tetrahedral grid is used as a basis to represent the electronic density, of a free or periodic system and Poisson's equation is solved as a boundary value problem. Nuclear cusps are treated using a local grid consisting of radial elements. These features facilitate the implementation of complicated energy functionals and permit a direct (constrained) energy minimization with respect to the density. We demonstrate the usefulness of the scheme by calculating the binding trends and polarizabilities of a number of atoms and molecules using a number of recently proposed non--local, orbital--free kinetic energy functionals^1,2. Scaling behavior, computational efficiency and the generalization to band--structure will also be discussed. indent 0 pt øbeylines øbeyspaces skip 0 pt ^1 P. Garcia-Gonzalez, J.E. Alvarellos and E. Chacon, Phys. Rev. B 54, 1897 (1996). ^2 A. J. Thakkar, Phys.Rev.B 46, 6920 (1992).

A fast parallel 3D Poisson solver with longitudinal periodic and transverse open boundary conditions for space-charge simulations

NASA Astrophysics Data System (ADS)

Qiang, Ji

2017-10-01

A three-dimensional (3D) Poisson solver with longitudinal periodic and transverse open boundary conditions can have important applications in beam physics of particle accelerators. In this paper, we present a fast efficient method to solve the Poisson equation using a spectral finite-difference method. This method uses a computational domain that contains the charged particle beam only and has a computational complexity of O(Nu(logNmode)) , where Nu is the total number of unknowns and Nmode is the maximum number of longitudinal or azimuthal modes. This saves both the computational time and the memory usage of using an artificial boundary condition in a large extended computational domain. The new 3D Poisson solver is parallelized using a message passing interface (MPI) on multi-processor computers and shows a reasonable parallel performance up to hundreds of processor cores.

Numerical algorithms based on Galerkin methods for the modeling of reactive interfaces in photoelectrochemical (PEC) solar cells

NASA Astrophysics Data System (ADS)

Harmon, Michael; Gamba, Irene M.; Ren, Kui

2016-12-01

This work concerns the numerical solution of a coupled system of self-consistent reaction-drift-diffusion-Poisson equations that describes the macroscopic dynamics of charge transport in photoelectrochemical (PEC) solar cells with reactive semiconductor and electrolyte interfaces. We present three numerical algorithms, mainly based on a mixed finite element and a local discontinuous Galerkin method for spatial discretization, with carefully chosen numerical fluxes, and implicit-explicit time stepping techniques, for solving the time-dependent nonlinear systems of partial differential equations. We perform computational simulations under various model parameters to demonstrate the performance of the proposed numerical algorithms as well as the impact of these parameters on the solution to the model.

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.

Phase field modeling of brittle fracture for enhanced assumed strain shells at large deformations: formulation and finite element implementation

NASA Astrophysics Data System (ADS)

Reinoso, J.; Paggi, M.; Linder, C.

2017-06-01

Fracture of technological thin-walled components can notably limit the performance of their corresponding engineering systems. With the aim of achieving reliable fracture predictions of thin structures, this work presents a new phase field model of brittle fracture for large deformation analysis of shells relying on a mixed enhanced assumed strain (EAS) formulation. The kinematic description of the shell body is constructed according to the solid shell concept. This enables the use of fully three-dimensional constitutive models for the material. The proposed phase field formulation integrates the use of the (EAS) method to alleviate locking pathologies, especially Poisson thickness and volumetric locking. This technique is further combined with the assumed natural strain method to efficiently derive a locking-free solid shell element. On the computational side, a fully coupled monolithic framework is consistently formulated. Specific details regarding the corresponding finite element formulation and the main aspects associated with its implementation in the general purpose packages FEAP and ABAQUS are addressed. Finally, the applicability of the current strategy is demonstrated through several numerical examples involving different loading conditions, and including linear and nonlinear hyperelastic constitutive models.

Comparison of robustness to outliers between robust poisson models and log-binomial models when estimating relative risks for common binary outcomes: a simulation study.

PubMed

Chen, Wansu; Shi, Jiaxiao; Qian, Lei; Azen, Stanley P

2014-06-26

To estimate relative risks or risk ratios for common binary outcomes, the most popular model-based methods are the robust (also known as modified) Poisson and the log-binomial regression. Of the two methods, it is believed that the log-binomial regression yields more efficient estimators because it is maximum likelihood based, while the robust Poisson model may be less affected by outliers. Evidence to support the robustness of robust Poisson models in comparison with log-binomial models is very limited. In this study a simulation was conducted to evaluate the performance of the two methods in several scenarios where outliers existed. The findings indicate that for data coming from a population where the relationship between the outcome and the covariate was in a simple form (e.g. log-linear), the two models yielded comparable biases and mean square errors. However, if the true relationship contained a higher order term, the robust Poisson models consistently outperformed the log-binomial models even when the level of contamination is low. The robust Poisson models are more robust (or less sensitive) to outliers compared to the log-binomial models when estimating relative risks or risk ratios for common binary outcomes. Users should be aware of the limitations when choosing appropriate models to estimate relative risks or risk ratios.

Nonlinear Poisson Equation for Heterogeneous Media

PubMed Central

Hu, Langhua; Wei, Guo-Wei

2012-01-01

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

A coarse-grid projection method for accelerating incompressible flow computations

NASA Astrophysics Data System (ADS)

San, Omer; Staples, Anne E.

2013-01-01

We present a coarse-grid projection (CGP) method for accelerating incompressible flow computations, which is applicable to methods involving Poisson equations as incompressibility constraints. The CGP methodology is a modular approach that facilitates data transfer with simple interpolations and uses black-box solvers for the Poisson and advection-diffusion equations in the flow solver. After solving the Poisson equation on a coarsened grid, an interpolation scheme is used to obtain the fine data for subsequent time stepping on the full grid. A particular version of the method is applied here to the vorticity-stream function, primitive variable, and vorticity-velocity formulations of incompressible Navier-Stokes equations. We compute several benchmark flow problems on two-dimensional Cartesian and non-Cartesian grids, as well as a three-dimensional flow problem. The method is found to accelerate these computations while retaining a level of accuracy close to that of the fine resolution field, which is significantly better than the accuracy obtained for a similar computation performed solely using a coarse grid. A linear acceleration rate is obtained for all the cases we consider due to the linear-cost elliptic Poisson solver used, with reduction factors in computational time between 2 and 42. The computational savings are larger when a suboptimal Poisson solver is used. We also find that the computational savings increase with increasing distortion ratio on non-Cartesian grids, making the CGP method a useful tool for accelerating generalized curvilinear incompressible flow solvers.

Response analysis of a class of quasi-linear systems with fractional derivative excited by Poisson white noise

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

Yang, Yongge; Xu, Wei, E-mail: weixu@nwpu.edu.cn; Yang, Guidong

The Poisson white noise, as a typical non-Gaussian excitation, has attracted much attention recently. However, little work was referred to the study of stochastic systems with fractional derivative under Poisson white noise excitation. This paper investigates the stationary response of a class of quasi-linear systems with fractional derivative excited by Poisson white noise. The equivalent stochastic system of the original stochastic system is obtained. Then, approximate stationary solutions are obtained with the help of the perturbation method. Finally, two typical examples are discussed in detail to demonstrate the effectiveness of the proposed method. The analysis also shows that the fractionalmore » order and the fractional coefficient significantly affect the responses of the stochastic systems with fractional derivative.« less

Monitoring Poisson observations using combined applications of Shewhart and EWMA charts

NASA Astrophysics Data System (ADS)

Abujiya, Mu'azu Ramat

2017-11-01

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

A System of Poisson Equations for a Nonconstant Varadhan Functional on a Finite State Space

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

Cavazos-Cadena, Rolando; Hernandez-Hernandez, Daniel

2006-01-15

Given a discrete-time Markov chain with finite state space and a stationary transition matrix, a system of 'local' Poisson equations characterizing the (exponential) Varadhan's functional J(.) is given. The main results, which are derived for an arbitrary transition structure so that J(.) may be nonconstant, are as follows: (i) Any solution to the local Poisson equations immediately renders Varadhan's functional, and (ii) a solution of the system always exist. The proof of this latter result is constructive and suggests a method to solve the local Poisson equations.

Marginalized zero-inflated Poisson models with missing covariates.

PubMed

Benecha, Habtamu K; Preisser, John S; Divaris, Kimon; Herring, Amy H; Das, Kalyan

2018-05-11

Unlike zero-inflated Poisson regression, marginalized zero-inflated Poisson (MZIP) models for counts with excess zeros provide estimates with direct interpretations for the overall effects of covariates on the marginal mean. In the presence of missing covariates, MZIP and many other count data models are ordinarily fitted using complete case analysis methods due to lack of appropriate statistical methods and software. This article presents an estimation method for MZIP models with missing covariates. The method, which is applicable to other missing data problems, is illustrated and compared with complete case analysis by using simulations and dental data on the caries preventive effects of a school-based fluoride mouthrinse program. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

An adaptively refined phase-space element method for cosmological simulations and collisionless dynamics

NASA Astrophysics Data System (ADS)

Hahn, Oliver; Angulo, Raul E.

2016-01-01

N-body simulations are essential for understanding the formation and evolution of structure in the Universe. However, the discrete nature of these simulations affects their accuracy when modelling collisionless systems. We introduce a new approach to simulate the gravitational evolution of cold collisionless fluids by solving the Vlasov-Poisson equations in terms of adaptively refineable `Lagrangian phase-space elements'. These geometrical elements are piecewise smooth maps between Lagrangian space and Eulerian phase-space and approximate the continuum structure of the distribution function. They allow for dynamical adaptive splitting to accurately follow the evolution even in regions of very strong mixing. We discuss in detail various one-, two- and three-dimensional test problems to demonstrate the performance of our method. Its advantages compared to N-body algorithms are: (I) explicit tracking of the fine-grained distribution function, (II) natural representation of caustics, (III) intrinsically smooth gravitational potential fields, thus (IV) eliminating the need for any type of ad hoc force softening. We show the potential of our method by simulating structure formation in a warm dark matter scenario. We discuss how spurious collisionality and large-scale discreteness noise of N-body methods are both strongly suppressed, which eliminates the artificial fragmentation of filaments. Therefore, we argue that our new approach improves on the N-body method when simulating self-gravitating cold and collisionless fluids, and is the first method that allows us to explicitly follow the fine-grained evolution in six-dimensional phase-space.

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.

Poisson-Gaussian Noise Analysis and Estimation for Low-Dose X-ray Images in the NSCT Domain.

PubMed

Lee, Sangyoon; Lee, Min Seok; Kang, Moon Gi

2018-03-29

The noise distribution of images obtained by X-ray sensors in low-dosage situations can be analyzed using the Poisson and Gaussian mixture model. Multiscale conversion is one of the most popular noise reduction methods used in recent years. Estimation of the noise distribution of each subband in the multiscale domain is the most important factor in performing noise reduction, with non-subsampled contourlet transform (NSCT) representing an effective method for scale and direction decomposition. In this study, we use artificially generated noise to analyze and estimate the Poisson-Gaussian noise of low-dose X-ray images in the NSCT domain. The noise distribution of the subband coefficients is analyzed using the noiseless low-band coefficients and the variance of the noisy subband coefficients. The noise-after-transform also follows a Poisson-Gaussian distribution, and the relationship between the noise parameters of the subband and the full-band image is identified. We then analyze noise of actual images to validate the theoretical analysis. Comparison of the proposed noise estimation method with an existing noise reduction method confirms that the proposed method outperforms traditional methods.

Stochastic Investigation of Natural Frequency for Functionally Graded Plates

NASA Astrophysics Data System (ADS)

Karsh, P. K.; Mukhopadhyay, T.; Dey, S.

2018-03-01

This paper presents the stochastic natural frequency analysis of functionally graded plates by applying artificial neural network (ANN) approach. Latin hypercube sampling is utilised to train the ANN model. The proposed algorithm for stochastic natural frequency analysis of FGM plates is validated and verified with original finite element method and Monte Carlo simulation (MCS). The combined stochastic variation of input parameters such as, elastic modulus, shear modulus, Poisson ratio, and mass density are considered. Power law is applied to distribute the material properties across the thickness. The present ANN model reduces the sample size and computationally found efficient as compared to conventional Monte Carlo simulation.

ANALYZING NUMERICAL ERRORS IN DOMAIN HEAT TRANSPORT MODELS USING THE CVBEM.

USGS Publications Warehouse

Hromadka, T.V.

1987-01-01

Besides providing an exact solution for steady-state heat conduction processes (Laplace-Poisson equations), the CVBEM (complex variable boundary element method) can be used for the numerical error analysis of domain model solutions. For problems where soil-water phase change latent heat effects dominate the thermal regime, heat transport can be approximately modeled as a time-stepped steady-state condition in the thawed and frozen regions, respectively. The CVBEM provides an exact solution of the two-dimensional steady-state heat transport problem, and also provides the error in matching the prescribed boundary conditions by the development of a modeling error distribution or an approximate boundary generation.

Expansion of the gravitational potential with computerized Poisson series

NASA Technical Reports Server (NTRS)

Broucke, R.

1976-01-01

The paper describes a recursive formulation for the expansion of the gravitational potential valid for both the tesseral and zonal harmonics. The expansion is primarily in rectangular coordinates, but the classical orbit elements or equinoctial orbit elements can be easily substituted. The equations of motion for the zonal harmonics in both classical and equinoctial orbital elements are described in a form which will result in closed-form expressions for the first-order perturbations. In order to achieve this result, the true longitude or true anomaly have to be used as independent variables.

ANALYZING NUMERICAL ERRORS IN DOMAIN HEAT TRANSPORT MODELS USING THE CVBEM.

USGS Publications Warehouse

Hromadka, T.V.; ,

1985-01-01

Besides providing an exact solution for steady-state heat conduction processes (Laplace Poisson equations), the CVBEM (complex variable boundary element method) can be used for the numerical error analysis of domain model solutions. For problems where soil water phase change latent heat effects dominate the thermal regime, heat transport can be approximately modeled as a time-stepped steady-state condition in the thawed and frozen regions, respectively. The CVBEM provides an exact solution of the two-dimensional steady-state heat transport problem, and also provides the error in matching the prescribed boundary conditions by the development of a modeling error distribution or an approximative boundary generation. This error evaluation can be used to develop highly accurate CVBEM models of the heat transport process, and the resulting model can be used as a test case for evaluating the precision of domain models based on finite elements or finite differences.

Finite element analysis of the influence of elastic anisotropy on stress intensification at stress corrosion cracking initiation sites in fcc alloys

NASA Astrophysics Data System (ADS)

Meric de Bellefon, G.; van Duysen, J. C.

2018-05-01

A recent finite-element method (FEM)-based study from the present authors quantified the effect of elastic anisotropy of grains on stress intensification at potential intergranular stress corrosion cracking (IGSCC) initiation sites in austenitic stainless steels. In particular, it showed that the auxetic behavior of grains (negative Poisson's ratio) in some directions plays a very important role in IGSCC initiation, since it can induce local stress intensification factors of about 1.6. A similar effect is expected for other fcc alloys such as Ni-based alloys. The present article confirms those results and paves the way to the definition of an IGSCC susceptibility index by identifying grain configurations that are the most favorable for crack initiation. The index will rely on the probability to get those configurations on surface of specimens.

Vectorized multigrid Poisson solver for the CDC CYBER 205

NASA Technical Reports Server (NTRS)

Barkai, D.; Brandt, M. A.

1984-01-01

The full multigrid (FMG) method is applied to the two dimensional Poisson equation with Dirichlet boundary conditions. This has been chosen as a relatively simple test case for examining the efficiency of fully vectorizing of the multigrid method. Data structure and programming considerations and techniques are discussed, accompanied by performance details.

Maximum-likelihood fitting of data dominated by Poisson statistical uncertainties

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

Stoneking, M.R.; Den Hartog, D.J.

1996-06-01

The fitting of data by {chi}{sup 2}-minimization is valid only when the uncertainties in the data are normally distributed. When analyzing spectroscopic or particle counting data at very low signal level (e.g., a Thomson scattering diagnostic), the uncertainties are distributed with a Poisson distribution. The authors have developed a maximum-likelihood method for fitting data that correctly treats the Poisson statistical character of the uncertainties. This method maximizes the total probability that the observed data are drawn from the assumed fit function using the Poisson probability function to determine the probability for each data point. The algorithm also returns uncertainty estimatesmore » for the fit parameters. They compare this method with a {chi}{sup 2}-minimization routine applied to both simulated and real data. Differences in the returned fits are greater at low signal level (less than {approximately}20 counts per measurement). the maximum-likelihood method is found to be more accurate and robust, returning a narrower distribution of values for the fit parameters with fewer outliers.« less

Matrix decomposition graphics processing unit solver for Poisson image editing

NASA Astrophysics Data System (ADS)

Lei, Zhao; Wei, Li

2012-10-01

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

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

NASA Astrophysics Data System (ADS)

Kim, Bongkeun; Song, Jiming; Song, Xueyu

2010-09-01

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

Noisy cooperative intermittent processes: From blinking quantum dots to human consciousness

NASA Astrophysics Data System (ADS)

Allegrini, Paolo; Paradisi, Paolo; Menicucci, Danilo; Bedini, Remo; Gemignani, Angelo; Fronzoni, Leone

2011-07-01

We study the superposition of a non-Poisson renewal process with the presence of a superimposed Poisson noise. The non-Poisson renewals mark the passage between meta-stable states in system with self-organization. We propose methods to measure the amount of information due to the two independent processes independently, and we see that a superficial study based on the survival probabilities yield stretched-exponential relaxations. Our method is in fact able to unravel the inverse-power law relaxation of the isolated non-Poisson processes, even when noise is present. We provide examples of this behavior in system of diverse nature, from blinking nano-crystals to weak turbulence. Finally we focus our discussion on events extracted from human electroencephalograms, and we discuss their connection with emerging properties of integrated neural dynamics, i.e. consciousness.

Tensorial Basis Spline Collocation Method for Poisson's Equation

NASA Astrophysics Data System (ADS)

Plagne, Laurent; Berthou, Jean-Yves

2000-01-01

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

Nonlinear Poisson equation for heterogeneous media.

PubMed

Hu, Langhua; Wei, Guo-Wei

2012-08-22

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

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

He, Yang; Xiao, Jianyuan; Zhang, Ruili

Hamiltonian time integrators for the Vlasov-Maxwell equations are developed by a Hamiltonian splitting technique. The Hamiltonian functional is split into five parts, which produces five exactly solvable subsystems. Each subsystem is a Hamiltonian system equipped with the Morrison-Marsden-Weinstein Poisson bracket. Compositions of the exact solutions provide Poisson structure preserving/Hamiltonian methods of arbitrary high order for the Vlasov-Maxwell equations. They are then accurate and conservative over a long time because of the Poisson-preserving nature.

Reduction of Poisson noise in measured time-resolved data for time-domain diffuse optical tomography.

PubMed

Okawa, S; Endo, Y; Hoshi, Y; Yamada, Y

2012-01-01

A method to reduce noise for time-domain diffuse optical tomography (DOT) is proposed. Poisson noise which contaminates time-resolved photon counting data is reduced by use of maximum a posteriori estimation. The noise-free data are modeled as a Markov random process, and the measured time-resolved data are assumed as Poisson distributed random variables. The posterior probability of the occurrence of the noise-free data is formulated. By maximizing the probability, the noise-free data are estimated, and the Poisson noise is reduced as a result. The performances of the Poisson noise reduction are demonstrated in some experiments of the image reconstruction of time-domain DOT. In simulations, the proposed method reduces the relative error between the noise-free and noisy data to about one thirtieth, and the reconstructed DOT image was smoothed by the proposed noise reduction. The variance of the reconstructed absorption coefficients decreased by 22% in a phantom experiment. The quality of DOT, which can be applied to breast cancer screening etc., is improved by the proposed noise reduction.

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

Evaluating the double Poisson generalized linear model.

PubMed

Zou, Yaotian; Geedipally, Srinivas Reddy; Lord, Dominique

2013-10-01

The objectives of this study are to: (1) examine the applicability of the double Poisson (DP) generalized linear model (GLM) for analyzing motor vehicle crash data characterized by over- and under-dispersion and (2) compare the performance of the DP GLM with the Conway-Maxwell-Poisson (COM-Poisson) GLM in terms of goodness-of-fit and theoretical soundness. The DP distribution has seldom been investigated and applied since its first introduction two decades ago. The hurdle for applying the DP is related to its normalizing constant (or multiplicative constant) which is not available in closed form. This study proposed a new method to approximate the normalizing constant of the DP with high accuracy and reliability. The DP GLM and COM-Poisson GLM were developed using two observed over-dispersed datasets and one observed under-dispersed dataset. The modeling results indicate that the DP GLM with its normalizing constant approximated by the new method can handle crash data characterized by over- and under-dispersion. Its performance is comparable to the COM-Poisson GLM in terms of goodness-of-fit (GOF), although COM-Poisson GLM provides a slightly better fit. For the over-dispersed data, the DP GLM performs similar to the NB GLM. Considering the fact that the DP GLM can be easily estimated with inexpensive computation and that it is simpler to interpret coefficients, it offers a flexible and efficient alternative for researchers to model count data. Copyright © 2013 Elsevier Ltd. All rights reserved.

Relative and Absolute Error Control in a Finite-Difference Method Solution of Poisson's Equation

ERIC Educational Resources Information Center

Prentice, J. S. C.

2012-01-01

An algorithm for error control (absolute and relative) in the five-point finite-difference method applied to Poisson's equation is described. The algorithm is based on discretization of the domain of the problem by means of three rectilinear grids, each of different resolution. We discuss some hardware limitations associated with the algorithm,…

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.

Efficiency optimization of a fast Poisson solver in beam dynamics simulation

NASA Astrophysics Data System (ADS)

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

2016-01-01

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

Improved Denoising via Poisson Mixture Modeling of Image Sensor Noise.

PubMed

Zhang, Jiachao; Hirakawa, Keigo

2017-04-01

This paper describes a study aimed at comparing the real image sensor noise distribution to the models of noise often assumed in image denoising designs. A quantile analysis in pixel, wavelet transform, and variance stabilization domains reveal that the tails of Poisson, signal-dependent Gaussian, and Poisson-Gaussian models are too short to capture real sensor noise behavior. A new Poisson mixture noise model is proposed to correct the mismatch of tail behavior. Based on the fact that noise model mismatch results in image denoising that undersmoothes real sensor data, we propose a mixture of Poisson denoising method to remove the denoising artifacts without affecting image details, such as edge and textures. Experiments with real sensor data verify that denoising for real image sensor data is indeed improved by this new technique.

Deterministic multidimensional nonuniform gap sampling.

PubMed

Worley, Bradley; Powers, Robert

2015-12-01

Born from empirical observations in nonuniformly sampled multidimensional NMR data relating to gaps between sampled points, the Poisson-gap sampling method has enjoyed widespread use in biomolecular NMR. While the majority of nonuniform sampling schemes are fully randomly drawn from probability densities that vary over a Nyquist grid, the Poisson-gap scheme employs constrained random deviates to minimize the gaps between sampled grid points. We describe a deterministic gap sampling method, based on the average behavior of Poisson-gap sampling, which performs comparably to its random counterpart with the additional benefit of completely deterministic behavior. We also introduce a general algorithm for multidimensional nonuniform sampling based on a gap equation, and apply it to yield a deterministic sampling scheme that combines burst-mode sampling features with those of Poisson-gap schemes. Finally, we derive a relationship between stochastic gap equations and the expectation value of their sampling probability densities. Copyright © 2015 Elsevier Inc. All rights reserved.

Nonlinear Finite Element Analysis of a General Composite Shell

DTIC Science & Technology

1988-12-01

strain I Poisson’s ratio ix I I iI I I 1 Total potential energy a Normal stress rShear stress Rotational terms Distance from midsurface e ,Y ,0 Rotations...respectively 0 0 Subscript "e" indicates element reference Subscript "g" indicates global reference Superscript "o" indicates midsurface values...surface strains and rotations are small, and displacements away from the midsurface are restricted by the Kirchhoff-Love hypotheses [3]. With these

Image Understanding Research.

DTIC Science & Technology

1978-09-30

element output sequence, and h is an L element impulse response sequence with M = N+L-l, and E (m) represents noise or - measurement uncertainty at the...William K. Pratt ......... 123 3.2 Estimation of Image Signal with Poisson Noise - I - Chun Moo Lo and Alexander A. Sawchuk ........ 135 3.3 Computer... noise ratio (SNR) of 10.0. From these curves, it is apparent that the Sobel and Prewitt 3 x 3 operators are superior to the Roberts 2 x 2 operators. The

Fuzzy classifier based support vector regression framework for Poisson ratio determination

NASA Astrophysics Data System (ADS)

Asoodeh, Mojtaba; Bagheripour, Parisa

2013-09-01

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

Poisson Regression Analysis of Illness and Injury Surveillance Data

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

Frome E.L., Watkins J.P., Ellis E.D.

2012-12-12

The Department of Energy (DOE) uses illness and injury surveillance to monitor morbidity and assess the overall health of the work force. Data collected from each participating site include health events and a roster file with demographic information. The source data files are maintained in a relational data base, and are used to obtain stratified tables of health event counts and person time at risk that serve as the starting point for Poisson regression analysis. The explanatory variables that define these tables are age, gender, occupational group, and time. Typical response variables of interest are the number of absences duemore » to illness or injury, i.e., the response variable is a count. Poisson regression methods are used to describe the effect of the explanatory variables on the health event rates using a log-linear main effects model. Results of fitting the main effects model are summarized in a tabular and graphical form and interpretation of model parameters is provided. An analysis of deviance table is used to evaluate the importance of each of the explanatory variables on the event rate of interest and to determine if interaction terms should be considered in the analysis. Although Poisson regression methods are widely used in the analysis of count data, there are situations in which over-dispersion occurs. This could be due to lack-of-fit of the regression model, extra-Poisson variation, or both. A score test statistic and regression diagnostics are used to identify over-dispersion. A quasi-likelihood method of moments procedure is used to evaluate and adjust for extra-Poisson variation when necessary. Two examples are presented using respiratory disease absence rates at two DOE sites to illustrate the methods and interpretation of the results. In the first example the Poisson main effects model is adequate. In the second example the score test indicates considerable over-dispersion and a more detailed analysis attributes the over-dispersion to extra-Poisson variation. The R open source software environment for statistical computing and graphics is used for analysis. Additional details about R and the data that were used in this report are provided in an Appendix. Information on how to obtain R and utility functions that can be used to duplicate results in this report are provided.« less

An automatic multigrid method for the solution of sparse linear systems

NASA Technical Reports Server (NTRS)

Shapira, Yair; Israeli, Moshe; Sidi, Avram

1993-01-01

An automatic version of the multigrid method for the solution of linear systems arising from the discretization of elliptic PDE's is presented. This version is based on the structure of the algebraic system solely, and does not use the original partial differential operator. Numerical experiments show that for the Poisson equation the rate of convergence of our method is equal to that of classical multigrid methods. Moreover, the method is robust in the sense that its high rate of convergence is conserved for other classes of problems: non-symmetric, hyperbolic (even with closed characteristics) and problems on non-uniform grids. No double discretization or special treatment of sub-domains (e.g. boundaries) is needed. When supplemented with a vector extrapolation method, high rates of convergence are achieved also for anisotropic and discontinuous problems and also for indefinite Helmholtz equations. A new double discretization strategy is proposed for finite and spectral element schemes and is found better than known strategies.

Acoustic and elastic waves in metamaterials for underwater applications

NASA Astrophysics Data System (ADS)

Titovich, Alexey S.

Elastic effects in acoustic metamaterials are investigated. Water-based periodic arrays of elastic scatterers, sonic crystals, suffer from low transmission due to the impedance and index mismatch of typical engineering materials with water. A new type of acoustic metamaterial element is proposed that can be tuned to match the acoustic properties of water in the quasi-static regime. The element comprises a hollow elastic cylindrical shell fitted with an optimized internal substructure consisting of a central mass supported by an axisymmetric distribution of elastic stiffeners, which dictate the shell's effective bulk modulus and density. The derived closed form scattering solution for this system shows that the subsonic flexural waves excited in the shell by the attachment of stiffeners are suppressed by including a sufficiently large number of such stiffeners. As an example of refraction-based wave steering, a cylindrical-to-plane wave lens is designed by varying the bulk modulus in the array according to the conformal mapping of a unit circle to a square. Elastic shells provide rich scattering properties, mainly due to their ability to support highly dispersive flexural waves. Analysis of flexural-borne waves on a pair of shells yields an analytical expression for the width of a flexural resonance, which is then used with the theory of multiple scattering to accurately predict the splitting of the resonance frequency. This analysis leads to the discovery of the acoustic Poisson-like effect in a periodic wave medium. This effect redirects an incident acoustic wave by 90° in an otherwise acoustically transparent sonic crystal. An unresponsive "deaf" antisymmetric mode locked to band gap boundaries is unlocked by matching Bragg scattering with a quadrupole flexural resonance of the shell. The dynamic effect causes normal unidirectional wave motion to strongly couple to perpendicular motion, analogous to the quasi-static Poisson effect in solids. The Poisson-like effect is demonstrated using the first flexural resonance of an acrylic shell. This represent a new type of material which cannot be accurately described as an effective acoustic medium. The study concludes with an analysis of a non-zero shear modulus in a pentamode cloak via the two-scale method with the shear modulus as the perturbation parameter.

Determination of confidence limits for experiments with low numbers of counts. [Poisson-distributed photon counts from astrophysical sources

NASA Technical Reports Server (NTRS)

Kraft, Ralph P.; Burrows, David N.; Nousek, John A.

1991-01-01

Two different methods, classical and Bayesian, for determining confidence intervals involving Poisson-distributed data are compared. Particular consideration is given to cases where the number of counts observed is small and is comparable to the mean number of background counts. Reasons for preferring the Bayesian over the classical method are given. Tables of confidence limits calculated by the Bayesian method are provided for quick reference.

Incompressible spectral-element method: Derivation of equations

NASA Technical Reports Server (NTRS)

Deanna, Russell G.

1993-01-01

A fractional-step splitting scheme breaks the full Navier-Stokes equations into explicit and implicit portions amenable to the calculus of variations. Beginning with the functional forms of the Poisson and Helmholtz equations, we substitute finite expansion series for the dependent variables and derive the matrix equations for the unknown expansion coefficients. This method employs a new splitting scheme which differs from conventional three-step (nonlinear, pressure, viscous) schemes. The nonlinear step appears in the conventional, explicit manner, the difference occurs in the pressure step. Instead of solving for the pressure gradient using the nonlinear velocity, we add the viscous portion of the Navier-Stokes equation from the previous time step to the velocity before solving for the pressure gradient. By combining this 'predicted' pressure gradient with the nonlinear velocity in an explicit term, and the Crank-Nicholson method for the viscous terms, we develop a Helmholtz equation for the final velocity.

Segmentation algorithm for non-stationary compound Poisson processes. With an application to inventory time series of market members in a financial market

NASA Astrophysics Data System (ADS)

Tóth, B.; Lillo, F.; Farmer, J. D.

2010-11-01

We introduce an algorithm for the segmentation of a class of regime switching processes. The segmentation algorithm is a non parametric statistical method able to identify the regimes (patches) of a time series. The process is composed of consecutive patches of variable length. In each patch the process is described by a stationary compound Poisson process, i.e. a Poisson process where each count is associated with a fluctuating signal. The parameters of the process are different in each patch and therefore the time series is non-stationary. Our method is a generalization of the algorithm introduced by Bernaola-Galván, et al. [Phys. Rev. Lett. 87, 168105 (2001)]. We show that the new algorithm outperforms the original one for regime switching models of compound Poisson processes. As an application we use the algorithm to segment the time series of the inventory of market members of the London Stock Exchange and we observe that our method finds almost three times more patches than the original one.

Numerical Solution of the Extended Nernst-Planck Model.

PubMed

Samson; Marchand

1999-07-01

The main features of a numerical model aiming at predicting the drift of ions in an electrolytic solution upon a chemical potential gradient are presented. The mechanisms of ionic diffusion are described by solving the extended Nernst-Planck system of equations. The electrical coupling between the various ionic fluxes is accounted for by the Poisson equation. Furthermore, chemical activity effects are considered in the model. The whole system of nonlinear equations is solved using the finite-element method. Results yielded by the model for simple test cases are compared to those obtained using an analytical solution. Applications of the model to more complex problems are also presented and discussed. Copyright 1999 Academic Press.

Differential expression analysis for RNAseq using Poisson mixed models

PubMed Central

Sun, Shiquan; Hood, Michelle; Scott, Laura; Peng, Qinke; Mukherjee, Sayan; Tung, Jenny

2017-01-01

Abstract Identifying differentially expressed (DE) genes from RNA sequencing (RNAseq) studies is among the most common analyses in genomics. However, RNAseq DE analysis presents several statistical and computational challenges, including over-dispersed read counts and, in some settings, sample non-independence. Previous count-based methods rely on simple hierarchical Poisson models (e.g. negative binomial) to model independent over-dispersion, but do not account for sample non-independence due to relatedness, population structure and/or hidden confounders. Here, we present a Poisson mixed model with two random effects terms that account for both independent over-dispersion and sample non-independence. We also develop a scalable sampling-based inference algorithm using a latent variable representation of the Poisson distribution. With simulations, we show that our method properly controls for type I error and is generally more powerful than other widely used approaches, except in small samples (n <15) with other unfavorable properties (e.g. small effect sizes). We also apply our method to three real datasets that contain related individuals, population stratification or hidden confounders. Our results show that our method increases power in all three data compared to other approaches, though the power gain is smallest in the smallest sample (n = 6). Our method is implemented in MACAU, freely available at www.xzlab.org/software.html. PMID:28369632

The Equivalence of Information-Theoretic and Likelihood-Based Methods for Neural Dimensionality Reduction

PubMed Central

Williamson, Ross S.; Sahani, Maneesh; Pillow, Jonathan W.

2015-01-01

Stimulus dimensionality-reduction methods in neuroscience seek to identify a low-dimensional space of stimulus features that affect a neuron’s probability of spiking. One popular method, known as maximally informative dimensions (MID), uses an information-theoretic quantity known as “single-spike information” to identify this space. Here we examine MID from a model-based perspective. We show that MID is a maximum-likelihood estimator for the parameters of a linear-nonlinear-Poisson (LNP) model, and that the empirical single-spike information corresponds to the normalized log-likelihood under a Poisson model. This equivalence implies that MID does not necessarily find maximally informative stimulus dimensions when spiking is not well described as Poisson. We provide several examples to illustrate this shortcoming, and derive a lower bound on the information lost when spiking is Bernoulli in discrete time bins. To overcome this limitation, we introduce model-based dimensionality reduction methods for neurons with non-Poisson firing statistics, and show that they can be framed equivalently in likelihood-based or information-theoretic terms. Finally, we show how to overcome practical limitations on the number of stimulus dimensions that MID can estimate by constraining the form of the non-parametric nonlinearity in an LNP model. We illustrate these methods with simulations and data from primate visual cortex. PMID:25831448

A Novel Method for Preparing Auxetic Foam from Closed-cell Polymer Foam Based on Steam Penetration and Condensation (SPC) Process.

PubMed

Fan, Donglei; Li, Minggang; Qiu, Jian; Xing, Haiping; Jiang, Zhiwei; Tang, Tao

2018-05-31

Auxetic materials are a class of materials possessing negative Poisson's ratio. Here we establish a novel method for preparing auxetic foam from closed-cell polymer foam based on steam penetration and condensation (SPC) process. Using polyethylene (PE) closed-cell foam as an example, the resultant foams treated by SPC process present negative Poisson's ratio during stretching and compression testing. The effect of steam-treated temperature and time on the conversion efficiency of negative Poisson's ratio foam is investigated, and the mechanism of SPC method for forming re-entrant structure is discussed. The results indicate that the presence of enough steam within the cells is a critical factor for the negative Poisson's ratio conversion in the SPC process. The pressure difference caused by steam condensation is the driving force for the conversion from conventional closed-cell foam to the negative Poisson's ratio foam. Furthermore, the applicability of SPC process for fabricating auxetic foam is studied by replacing PE foam by polyvinyl chloride (PVC) foam with closed-cell structure or replacing water steam by ethanol steam. The results verify the universality of SPC process for fabricating auxetic foams from conventional foams with closed-cell structure. In addition, we explored potential application of the obtained auxetic foams by SPC process in the fabrication of shape memory polymer materials.

Accurate solution of the Poisson equation with discontinuities

NASA Astrophysics Data System (ADS)

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

2017-11-01

Solving the Poisson equation in the presence of discontinuities is of great importance in many applications of science and engineering. In many cases, the discontinuities are caused by interfaces between different media, such as in multiphase flows. These interfaces are themselves solutions to differential equations, and can assume complex configurations. For this reason, it is convenient to embed the interface into a regular triangulation or Cartesian grid and solve the Poisson equation in this regular domain. We present an extension of the Correction Function Method (CFM), which was developed to solve the Poisson equation in the context of embedded interfaces. The distinctive feature of the CFM is that it uses partial differential equations to construct smooth extensions of the solution in the vicinity of interfaces. A consequence of this approach is that it can achieve high order of accuracy while maintaining compact discretizations. The extension we present removes the restrictions of the original CFM, and yields a method that can solve the Poisson equation when discontinuities are present in the solution, the coefficients of the equation (material properties), and the source term. We show results computed to fourth order of accuracy in two and three dimensions. This work was partially funded by DARPA, NSF, and NSERC.

A new multivariate zero-adjusted Poisson model with applications to biomedicine.

PubMed

Liu, Yin; Tian, Guo-Liang; Tang, Man-Lai; Yuen, Kam Chuen

2018-05-25

Recently, although advances were made on modeling multivariate count data, existing models really has several limitations: (i) The multivariate Poisson log-normal model (Aitchison and Ho, ) cannot be used to fit multivariate count data with excess zero-vectors; (ii) The multivariate zero-inflated Poisson (ZIP) distribution (Li et al., 1999) cannot be used to model zero-truncated/deflated count data and it is difficult to apply to high-dimensional cases; (iii) The Type I multivariate zero-adjusted Poisson (ZAP) distribution (Tian et al., 2017) could only model multivariate count data with a special correlation structure for random components that are all positive or negative. In this paper, we first introduce a new multivariate ZAP distribution, based on a multivariate Poisson distribution, which allows the correlations between components with a more flexible dependency structure, that is some of the correlation coefficients could be positive while others could be negative. We then develop its important distributional properties, and provide efficient statistical inference methods for multivariate ZAP model with or without covariates. Two real data examples in biomedicine are used to illustrate the proposed methods. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

The accurate solution of Poisson's equation by expansion in Chebyshev polynomials

NASA Technical Reports Server (NTRS)

Haidvogel, D. B.; Zang, T.

1979-01-01

A Chebyshev expansion technique is applied to Poisson's equation on a square with homogeneous Dirichlet boundary conditions. The spectral equations are solved in two ways - by alternating direction and by matrix diagonalization methods. Solutions are sought to both oscillatory and mildly singular problems. The accuracy and efficiency of the Chebyshev approach compare favorably with those of standard second- and fourth-order finite-difference methods.

On the Determination of Poisson Statistics for Haystack Radar Observations of Orbital Debris

NASA Technical Reports Server (NTRS)

Stokely, Christopher L.; Benbrook, James R.; Horstman, Matt

2007-01-01

A convenient and powerful method is used to determine if radar detections of orbital debris are observed according to Poisson statistics. This is done by analyzing the time interval between detection events. For Poisson statistics, the probability distribution of the time interval between events is shown to be an exponential distribution. This distribution is a special case of the Erlang distribution that is used in estimating traffic loads on telecommunication networks. Poisson statistics form the basis of many orbital debris models but the statistical basis of these models has not been clearly demonstrated empirically until now. Interestingly, during the fiscal year 2003 observations with the Haystack radar in a fixed staring mode, there are no statistically significant deviations observed from that expected with Poisson statistics, either independent or dependent of altitude or inclination. One would potentially expect some significant clustering of events in time as a result of satellite breakups, but the presence of Poisson statistics indicates that such debris disperse rapidly with respect to Haystack's very narrow radar beam. An exception to Poisson statistics is observed in the months following the intentional breakup of the Fengyun satellite in January 2007.

Bayesian inference on multiscale models for poisson intensity estimation: applications to photon-limited image denoising.

PubMed

Lefkimmiatis, Stamatios; Maragos, Petros; Papandreou, George

2009-08-01

We present an improved statistical model for analyzing Poisson processes, with applications to photon-limited imaging. We build on previous work, adopting a multiscale representation of the Poisson process in which the ratios of the underlying Poisson intensities (rates) in adjacent scales are modeled as mixtures of conjugate parametric distributions. Our main contributions include: 1) a rigorous and robust regularized expectation-maximization (EM) algorithm for maximum-likelihood estimation of the rate-ratio density parameters directly from the noisy observed Poisson data (counts); 2) extension of the method to work under a multiscale hidden Markov tree model (HMT) which couples the mixture label assignments in consecutive scales, thus modeling interscale coefficient dependencies in the vicinity of image edges; 3) exploration of a 2-D recursive quad-tree image representation, involving Dirichlet-mixture rate-ratio densities, instead of the conventional separable binary-tree image representation involving beta-mixture rate-ratio densities; and 4) a novel multiscale image representation, which we term Poisson-Haar decomposition, that better models the image edge structure, thus yielding improved performance. Experimental results on standard images with artificially simulated Poisson noise and on real photon-limited images demonstrate the effectiveness of the proposed techniques.

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

The scaling of oblique plasma double layers

NASA Technical Reports Server (NTRS)

Borovsky, J. E.

1983-01-01

Strong oblique plasma double layers are investigated using three methods, i.e., electrostatic particle-in-cell simulations, numerical solutions to the Poisson-Vlasov equations, and analytical approximations to the Poisson-Vlasov equations. The solutions to the Poisson-Vlasov equations and numerical simulations show that strong oblique double layers scale in terms of Debye lengths. For very large potential jumps, theory and numerical solutions indicate that all effects of the magnetic field vanish and the oblique double layers follow the same scaling relation as the field-aligned double layers.

Characterizing the performance of the Conway-Maxwell Poisson generalized linear model.

PubMed

Francis, Royce A; Geedipally, Srinivas Reddy; Guikema, Seth D; Dhavala, Soma Sekhar; Lord, Dominique; LaRocca, Sarah

2012-01-01

Count data are pervasive in many areas of risk analysis; deaths, adverse health outcomes, infrastructure system failures, and traffic accidents are all recorded as count events, for example. Risk analysts often wish to estimate the probability distribution for the number of discrete events as part of doing a risk assessment. Traditional count data regression models of the type often used in risk assessment for this problem suffer from limitations due to the assumed variance structure. A more flexible model based on the Conway-Maxwell Poisson (COM-Poisson) distribution was recently proposed, a model that has the potential to overcome the limitations of the traditional model. However, the statistical performance of this new model has not yet been fully characterized. This article assesses the performance of a maximum likelihood estimation method for fitting the COM-Poisson generalized linear model (GLM). The objectives of this article are to (1) characterize the parameter estimation accuracy of the MLE implementation of the COM-Poisson GLM, and (2) estimate the prediction accuracy of the COM-Poisson GLM using simulated data sets. The results of the study indicate that the COM-Poisson GLM is flexible enough to model under-, equi-, and overdispersed data sets with different sample mean values. The results also show that the COM-Poisson GLM yields accurate parameter estimates. The COM-Poisson GLM provides a promising and flexible approach for performing count data regression. © 2011 Society for Risk Analysis.

Application of Poisson random effect models for highway network screening.

PubMed

Jiang, Ximiao; Abdel-Aty, Mohamed; Alamili, Samer

2014-02-01

In recent years, Bayesian random effect models that account for the temporal and spatial correlations of crash data became popular in traffic safety research. This study employs random effect Poisson Log-Normal models for crash risk hotspot identification. Both the temporal and spatial correlations of crash data were considered. Potential for Safety Improvement (PSI) were adopted as a measure of the crash risk. Using the fatal and injury crashes that occurred on urban 4-lane divided arterials from 2006 to 2009 in the Central Florida area, the random effect approaches were compared to the traditional Empirical Bayesian (EB) method and the conventional Bayesian Poisson Log-Normal model. A series of method examination tests were conducted to evaluate the performance of different approaches. These tests include the previously developed site consistence test, method consistence test, total rank difference test, and the modified total score test, as well as the newly proposed total safety performance measure difference test. Results show that the Bayesian Poisson model accounting for both temporal and spatial random effects (PTSRE) outperforms the model that with only temporal random effect, and both are superior to the conventional Poisson Log-Normal model (PLN) and the EB model in the fitting of crash data. Additionally, the method evaluation tests indicate that the PTSRE model is significantly superior to the PLN model and the EB model in consistently identifying hotspots during successive time periods. The results suggest that the PTSRE model is a superior alternative for road site crash risk hotspot identification. Copyright © 2013 Elsevier Ltd. All rights reserved.

A dictionary learning approach for Poisson image deblurring.

PubMed

Ma, Liyan; Moisan, Lionel; Yu, Jian; Zeng, Tieyong

2013-07-01

The restoration of images corrupted by blur and Poisson noise is a key issue in medical and biological image processing. While most existing methods are based on variational models, generally derived from a maximum a posteriori (MAP) formulation, recently sparse representations of images have shown to be efficient approaches for image recovery. Following this idea, we propose in this paper a model containing three terms: a patch-based sparse representation prior over a learned dictionary, the pixel-based total variation regularization term and a data-fidelity term capturing the statistics of Poisson noise. The resulting optimization problem can be solved by an alternating minimization technique combined with variable splitting. Extensive experimental results suggest that in terms of visual quality, peak signal-to-noise ratio value and the method noise, the proposed algorithm outperforms state-of-the-art methods.

Integer lattice gas with Monte Carlo collision operator recovers the lattice Boltzmann method with Poisson-distributed fluctuations

NASA Astrophysics Data System (ADS)

Blommel, Thomas; Wagner, Alexander J.

2018-02-01

We examine a new kind of lattice gas that closely resembles modern lattice Boltzmann methods. This new kind of lattice gas, which we call a Monte Carlo lattice gas, has interesting properties that shed light on the origin of the multirelaxation time collision operator, and it derives the equilibrium distribution for an entropic lattice Boltzmann. Furthermore these lattice gas methods have Galilean invariant fluctuations given by a Poisson statistics, giving further insight into the properties that we should expect for fluctuating lattice Boltzmann methods.

Beyond single-stream with the Schrödinger method

NASA Astrophysics Data System (ADS)

Uhlemann, Cora; Kopp, Michael

2016-10-01

We investigate large scale structure formation of collisionless dark matter in the phase space description based on the Vlasov-Poisson equation. We present the Schrödinger method, originally proposed by \\cite{WK93} as numerical technique based on the Schrödinger Poisson equation, as an analytical tool which is superior to the common standard pressureless fluid model. Whereas the dust model fails and develops singularities at shell crossing the Schrödinger method encompasses multi-streaming and even virialization.

Poisson regression models outperform the geometrical model in estimating the peak-to-trough ratio of seasonal variation: a simulation study.

PubMed

Christensen, A L; Lundbye-Christensen, S; Dethlefsen, C

2011-12-01

Several statistical methods of assessing seasonal variation are available. Brookhart and Rothman [3] proposed a second-order moment-based estimator based on the geometrical model derived by Edwards [1], and reported that this estimator is superior in estimating the peak-to-trough ratio of seasonal variation compared with Edwards' estimator with respect to bias and mean squared error. Alternatively, seasonal variation may be modelled using a Poisson regression model, which provides flexibility in modelling the pattern of seasonal variation and adjustments for covariates. Based on a Monte Carlo simulation study three estimators, one based on the geometrical model, and two based on log-linear Poisson regression models, were evaluated in regards to bias and standard deviation (SD). We evaluated the estimators on data simulated according to schemes varying in seasonal variation and presence of a secular trend. All methods and analyses in this paper are available in the R package Peak2Trough[13]. Applying a Poisson regression model resulted in lower absolute bias and SD for data simulated according to the corresponding model assumptions. Poisson regression models had lower bias and SD for data simulated to deviate from the corresponding model assumptions than the geometrical model. This simulation study encourages the use of Poisson regression models in estimating the peak-to-trough ratio of seasonal variation as opposed to the geometrical model. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

Application of the Conway-Maxwell-Poisson generalized linear model for analyzing motor vehicle crashes.

PubMed

Lord, Dominique; Guikema, Seth D; Geedipally, Srinivas Reddy

2008-05-01

This paper documents the application of the Conway-Maxwell-Poisson (COM-Poisson) generalized linear model (GLM) for modeling motor vehicle crashes. The COM-Poisson distribution, originally developed in 1962, has recently been re-introduced by statisticians for analyzing count data subjected to over- and under-dispersion. This innovative distribution is an extension of the Poisson distribution. The objectives of this study were to evaluate the application of the COM-Poisson GLM for analyzing motor vehicle crashes and compare the results with the traditional negative binomial (NB) model. The comparison analysis was carried out using the most common functional forms employed by transportation safety analysts, which link crashes to the entering flows at intersections or on segments. To accomplish the objectives of the study, several NB and COM-Poisson GLMs were developed and compared using two datasets. The first dataset contained crash data collected at signalized four-legged intersections in Toronto, Ont. The second dataset included data collected for rural four-lane divided and undivided highways in Texas. Several methods were used to assess the statistical fit and predictive performance of the models. The results of this study show that COM-Poisson GLMs perform as well as NB models in terms of GOF statistics and predictive performance. Given the fact the COM-Poisson distribution can also handle under-dispersed data (while the NB distribution cannot or has difficulties converging), which have sometimes been observed in crash databases, the COM-Poisson GLM offers a better alternative over the NB model for modeling motor vehicle crashes, especially given the important limitations recently documented in the safety literature about the latter type of model.

A special case of the Poisson PDE formulated for Earth's surface and its capability to approximate the terrain mass density employing land-based gravity data, a case study in the south of Iran

NASA Astrophysics Data System (ADS)

AllahTavakoli, Yahya; Safari, Abdolreza; Vaníček, Petr

2016-12-01

This paper resurrects a version of Poisson's Partial Differential Equation (PDE) associated with the gravitational field at the Earth's surface and illustrates how the PDE possesses a capability to extract the mass density of Earth's topography from land-based gravity data. Herein, first we propound a theorem which mathematically introduces this version of Poisson's PDE adapted for the Earth's surface and then we use this PDE to develop a method of approximating the terrain mass density. Also, we carry out a real case study showing how the proposed approach is able to be applied to a set of land-based gravity data. In the case study, the method is summarized by an algorithm and applied to a set of gravity stations located along a part of the north coast of the Persian Gulf in the south of Iran. The results were numerically validated via rock-samplings as well as a geological map. Also, the method was compared with two conventional methods of mass density reduction. The numerical experiments indicate that the Poisson PDE at the Earth's surface has the capability to extract the mass density from land-based gravity data and is able to provide an alternative and somewhat more precise method of estimating the terrain mass density.

Differential expression analysis for RNAseq using Poisson mixed models.

PubMed

Sun, Shiquan; Hood, Michelle; Scott, Laura; Peng, Qinke; Mukherjee, Sayan; Tung, Jenny; Zhou, Xiang

2017-06-20

Identifying differentially expressed (DE) genes from RNA sequencing (RNAseq) studies is among the most common analyses in genomics. However, RNAseq DE analysis presents several statistical and computational challenges, including over-dispersed read counts and, in some settings, sample non-independence. Previous count-based methods rely on simple hierarchical Poisson models (e.g. negative binomial) to model independent over-dispersion, but do not account for sample non-independence due to relatedness, population structure and/or hidden confounders. Here, we present a Poisson mixed model with two random effects terms that account for both independent over-dispersion and sample non-independence. We also develop a scalable sampling-based inference algorithm using a latent variable representation of the Poisson distribution. With simulations, we show that our method properly controls for type I error and is generally more powerful than other widely used approaches, except in small samples (n <15) with other unfavorable properties (e.g. small effect sizes). We also apply our method to three real datasets that contain related individuals, population stratification or hidden confounders. Our results show that our method increases power in all three data compared to other approaches, though the power gain is smallest in the smallest sample (n = 6). Our method is implemented in MACAU, freely available at www.xzlab.org/software.html. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Measuring Poisson Ratios at Low Temperatures

NASA Technical Reports Server (NTRS)

Boozon, R. S.; Shepic, J. A.

1987-01-01

Simple extensometer ring measures bulges of specimens in compression. New method of measuring Poisson's ratio used on brittle ceramic materials at cryogenic temperatures. Extensometer ring encircles cylindrical specimen. Four strain gauges connected in fully active Wheatstone bridge self-temperature-compensating. Used at temperatures as low as liquid helium.

Dynamics of a prey-predator system under Poisson white noise excitation

NASA Astrophysics Data System (ADS)

Pan, Shan-Shan; Zhu, Wei-Qiu

2014-10-01

The classical Lotka-Volterra (LV) model is a well-known mathematical model for prey-predator ecosystems. In the present paper, the pulse-type version of stochastic LV model, in which the effect of a random natural environment has been modeled as Poisson white noise, is investigated by using the stochastic averaging method. The averaged generalized Itô stochastic differential equation and Fokker-Planck-Kolmogorov (FPK) equation are derived for prey-predator ecosystem driven by Poisson white noise. Approximate stationary solution for the averaged generalized FPK equation is obtained by using the perturbation method. The effect of prey self-competition parameter ɛ2 s on ecosystem behavior is evaluated. The analytical result is confirmed by corresponding Monte Carlo (MC) simulation.

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

NASA Technical Reports Server (NTRS)

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

1986-01-01

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

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.

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.

Poisson-Boltzmann theory of the charge-induced adsorption of semi-flexible polyelectrolytes.

PubMed

Ubbink, Job; Khokhlov, Alexei R

2004-03-15

A model is suggested for the structure of an adsorbed layer of a highly charged semi-flexible polyelectrolyte on a weakly charged surface of opposite charge sign. The adsorbed phase is thin, owing to the effective reversal of the charge sign of the surface upon adsorption, and ordered, owing to the high surface density of polyelectrolyte strands caused by the generally strong binding between polyelectrolyte and surface. The Poisson-Boltzmann equation for the electrostatic interaction between the array of adsorbed polyelectrolytes and the charged surface is solved for a cylindrical geometry, both numerically, using a finite element method, and analytically within the weak curvature limit under the assumption of excess monovalent salt. For small separations, repulsive surface polarization and counterion osmotic pressure effects dominate over the electrostatic attraction and the resulting electrostatic interaction curve shows a minimum at nonzero separations on the Angstrom scale. The equilibrium density of the adsorbed phase is obtained by minimizing the total free energy under the condition of equality of chemical potential and osmotic pressure of the polyelectrolyte in solution and in the adsorbed phase. For a wide range of ionic conditions and charge densities of the charged surface, the interstrand separation as predicted by the Poisson-Boltzmann model and the analytical theory closely agree. For low to moderate charge densities of the adsorbing surface, the interstrand spacing decreases as a function of the charge density of the charged surface. Above about 0.1 M excess monovalent salt, it is only weakly dependent on the ionic strength. At high charge densities of the adsorbing surface, the interstrand spacing increases with increasing ionic strength, in line with the experiments by Fang and Yang [J. Phys. Chem. B 101, 441 (1997)]. (c) 2004 American Institute of Physics.

A novel slithering locomotion mechanism for a snake-like soft robot

NASA Astrophysics Data System (ADS)

Cao, Yunteng; Liu, Yilun; Chen, Youlong; Zhu, Liangliang; Yan, Yuan; Chen, Xi

2017-02-01

A novel mechanism for slithering locomotion of a snake-like soft robot is presented. A rectangular beam with an isotropic coefficient of friction of its contact surface with the flat ground can move forward or backward when actuated by a periodic traveling sinusoidal wave. The Poisson's ratio of the beam plays an important role in the slithering locomotion speed and direction, particularly when it is negative. A theoretical model is proposed to elucidate the slithering locomotion mechanism, which is analogous to the rolling of a wheel on ground. There are two key factors of slithering locomotion: a rotational velocity field and a corresponding local contact region between the beam and ground. During wriggling motion of the rectangular beam, a rotational velocity field is observed near the maximum curvature point of the beam. If the beam has a negative Poisson's ratio, the axial tension will cause a lateral expansion so that the contact region between the beam and ground is located at the outer edge of the maximum curvature (the largest lateral expansion point). The direction of the beam's velocity at this outer edge is usually opposite to the traveling wave direction, so the friction force propels the beam in the direction of the traveling wave. A similar scenario is found for the relatively large amplitude of wriggling motion when the beam's Poisson's ratio is positive. Finite element method (FEM) simulation was conducted to verify the slithering locomotion mechanism, and good agreement was found between the FEM simulation results and theoretical predictions. The insights obtained here present a simple, novel and straightforward mechanism for slithering locomotion and are helpful for future designs of snake-like soft robots.

Analysis of warping deformation modes using higher order ANCF beam element

NASA Astrophysics Data System (ADS)

Orzechowski, Grzegorz; Shabana, Ahmed A.

2016-02-01

Most classical beam theories assume that the beam cross section remains a rigid surface under an arbitrary loading condition. However, in the absolute nodal coordinate formulation (ANCF) continuum-based beams, this assumption can be relaxed allowing for capturing deformation modes that couple the cross-section deformation and beam bending, torsion, and/or elongation. The deformation modes captured by ANCF finite elements depend on the interpolating polynomials used. The most widely used spatial ANCF beam element employs linear approximation in the transverse direction, thereby restricting the cross section deformation and leading to locking problems. The objective of this investigation is to examine the behavior of a higher order ANCF beam element that includes quadratic interpolation in the transverse directions. This higher order element allows capturing warping and non-uniform stretching distribution. Furthermore, this higher order element allows for increasing the degree of continuity at the element interface. It is shown in this paper that the higher order ANCF beam element can be used effectively to capture warping and eliminate Poisson locking that characterizes lower order ANCF finite elements. It is also shown that increasing the degree of continuity requires a special attention in order to have acceptable results. Because higher order elements can be more computationally expensive than the lower order elements, the use of reduced integration for evaluating the stress forces and the use of explicit and implicit numerical integrations to solve the nonlinear dynamic equations of motion are investigated in this paper. It is shown that the use of some of these integration methods can be very effective in reducing the CPU time without adversely affecting the solution accuracy.

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.

Accurate Solution of Multi-Region Continuum Biomolecule Electrostatic Problems Using the Linearized Poisson-Boltzmann Equation with Curved Boundary Elements

PubMed Central

Altman, Michael D.; Bardhan, Jaydeep P.; White, Jacob K.; Tidor, Bruce

2009-01-01

We present a boundary-element method (BEM) implementation for accurately solving problems in biomolecular electrostatics using the linearized Poisson–Boltzmann equation. Motivating this implementation is the desire to create a solver capable of precisely describing the geometries and topologies prevalent in continuum models of biological molecules. This implementation is enabled by the synthesis of four technologies developed or implemented specifically for this work. First, molecular and accessible surfaces used to describe dielectric and ion-exclusion boundaries were discretized with curved boundary elements that faithfully reproduce molecular geometries. Second, we avoided explicitly forming the dense BEM matrices and instead solved the linear systems with a preconditioned iterative method (GMRES), using a matrix compression algorithm (FFTSVD) to accelerate matrix-vector multiplication. Third, robust numerical integration methods were employed to accurately evaluate singular and near-singular integrals over the curved boundary elements. Finally, we present a general boundary-integral approach capable of modeling an arbitrary number of embedded homogeneous dielectric regions with differing dielectric constants, possible salt treatment, and point charges. A comparison of the presented BEM implementation and standard finite-difference techniques demonstrates that for certain classes of electrostatic calculations, such as determining absolute electrostatic solvation and rigid-binding free energies, the improved convergence properties of the BEM approach can have a significant impact on computed energetics. We also demonstrate that the improved accuracy offered by the curved-element BEM is important when more sophisticated techniques, such as non-rigid-binding models, are used to compute the relative electrostatic effects of molecular modifications. In addition, we show that electrostatic calculations requiring multiple solves using the same molecular geometry, such as charge optimization or component analysis, can be computed to high accuracy using the presented BEM approach, in compute times comparable to traditional finite-difference methods. PMID:18567005

Adaptive and iterative methods for simulations of nanopores with the PNP-Stokes equations

NASA Astrophysics Data System (ADS)

Mitscha-Baude, Gregor; Buttinger-Kreuzhuber, Andreas; Tulzer, Gerhard; Heitzinger, Clemens

2017-06-01

We present a 3D finite element solver for the nonlinear Poisson-Nernst-Planck (PNP) equations for electrodiffusion, coupled to the Stokes system of fluid dynamics. The model serves as a building block for the simulation of macromolecule dynamics inside nanopore sensors. The source code is released online at http://github.com/mitschabaude/nanopores. We add to existing numerical approaches by deploying goal-oriented adaptive mesh refinement. To reduce the computation overhead of mesh adaptivity, our error estimator uses the much cheaper Poisson-Boltzmann equation as a simplified model, which is justified on heuristic grounds but shown to work well in practice. To address the nonlinearity in the full PNP-Stokes system, three different linearization schemes are proposed and investigated, with two segregated iterative approaches both outperforming a naive application of Newton's method. Numerical experiments are reported on a real-world nanopore sensor geometry. We also investigate two different models for the interaction of target molecules with the nanopore sensor through the PNP-Stokes equations. In one model, the molecule is of finite size and is explicitly built into the geometry; while in the other, the molecule is located at a single point and only modeled implicitly - after solution of the system - which is computationally favorable. We compare the resulting force profiles of the electric and velocity fields acting on the molecule, and conclude that the point-size model fails to capture important physical effects such as the dependence of charge selectivity of the sensor on the molecule radius.

Functionally-fitted energy-preserving integrators for Poisson systems

NASA Astrophysics Data System (ADS)

Wang, Bin; Wu, Xinyuan

2018-07-01

In this paper, a new class of energy-preserving integrators is proposed and analysed for Poisson systems by using functionally-fitted technology. The integrators exactly preserve energy and have arbitrarily high order. It is shown that the proposed approach allows us to obtain the energy-preserving methods derived in [12] by Cohen and Hairer (2011) and in [1] by Brugnano et al. (2012) for Poisson systems. Furthermore, we study the sufficient conditions that ensure the existence of a unique solution and discuss the order of the new energy-preserving integrators.

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.

Evaluation of Shiryaev-Roberts procedure for on-line environmental radiation monitoring.

PubMed

Watson, Mara M; Seliman, Ayman F; Bliznyuk, Valery N; DeVol, Timothy A

2018-04-30

Water can become contaminated as a result of a leak from a nuclear facility, such as a waste facility, or from clandestine nuclear activity. Low-level on-line radiation monitoring is needed to detect these events in real time. A Bayesian control chart method, Shiryaev-Roberts (SR) procedure, was compared with classical methods, 3-σ and cumulative sum (CUSUM), for quantifying an accumulating signal from an extractive scintillating resin flow-cell detection system. Solutions containing 0.10-5.0 Bq/L of 99 Tc, as T99cO 4 - were pumped through a flow cell packed with extractive scintillating resin used in conjunction with a Beta-RAM Model 5 HPLC detector. While T99cO 4 - accumulated on the resin, time series data were collected. Control chart methods were applied to the data using statistical algorithms developed in MATLAB. SR charts were constructed using Poisson (Poisson SR) and Gaussian (Gaussian SR) probability distributions of count data to estimate the likelihood ratio. Poisson and Gaussian SR charts required less volume of radioactive solution at a fixed concentration to exceed the control limit in most cases than 3-σ and CUSUM control charts, particularly solutions with lower activity. SR is thus the ideal control chart for low-level on-line radiation monitoring. Once the control limit was exceeded, activity concentrations were estimated from the SR control chart using the control chart slope on a semi-logarithmic plot. A linear regression fit was applied to averaged slope data for five activity concentration groupings for Poisson and Gaussian SR control charts. A correlation coefficient (R 2 ) of 0.77 for Poisson SR and 0.90 for Gaussian SR suggest this method will adequately estimate activity concentration for an unknown solution. Copyright © 2018 Elsevier Ltd. All rights reserved.

A new approach to implement absorbing boundary condition in biomolecular electrostatics.

PubMed

Goni, Md Osman

2013-01-01

This paper discusses a novel approach to employ the absorbing boundary condition in conjunction with the finite-element method (FEM) in biomolecular electrostatics. The introduction of Bayliss-Turkel absorbing boundary operators in electromagnetic scattering problem has been incorporated by few researchers. However, in the area of biomolecular electrostatics, this boundary condition has not been investigated yet. The objective of this paper is twofold. First, to solve nonlinear Poisson-Boltzmann equation using Newton's method and second, to find an efficient and acceptable solution with minimum number of unknowns. In this work, a Galerkin finite-element formulation is used along with a Bayliss-Turkel absorbing boundary operator that explicitly accounts for the open field problem by mapping the Sommerfeld radiation condition from the far field to near field. While the Bayliss-Turkel condition works well when the artificial boundary is far from the scatterer, an acceptable tolerance of error can be achieved with the second order operator. Numerical results on test case with simple sphere show that the treatment is able to reach the same level of accuracy achieved by the analytical method while using a lower grid density. Bayliss-Turkel absorbing boundary condition (BTABC) combined with the FEM converges to the exact solution of scattering problems to within discretization error.

Fluid-structure interaction with pipe-wall viscoelasticity during water hammer

NASA Astrophysics Data System (ADS)

Keramat, A.; Tijsseling, A. S.; Hou, Q.; Ahmadi, A.

2012-01-01

Fluid-structure interaction (FSI) due to water hammer in a pipeline which has viscoelastic wall behaviour is studied. Appropriate governing equations are derived and numerically solved. In the numerical implementation of the hydraulic and structural equations, viscoelasticity is incorporated using the Kelvin-Voigt mechanical model. The equations are solved by two different approaches, namely the Method of Characteristics-Finite Element Method (MOC-FEM) and full MOC. In both approaches two important effects of FSI in fluid-filled pipes, namely Poisson and junction coupling, are taken into account. The study proposes a more comprehensive model for studying fluid transients in pipelines as compared to previous works, which take into account either FSI or viscoelasticity. To verify the proposed mathematical model and its numerical solutions, the following problems are investigated: axial vibration of a viscoelastic bar subjected to a step uniaxial loading, FSI in an elastic pipe, and hydraulic transients in a pressurised polyethylene pipe without FSI. The results of each case are checked with available exact and experimental results. Then, to study the simultaneous effects of FSI and viscoelasticity, which is the new element of the present research, one problem is solved by the two different numerical approaches. Both numerical methods give the same results, thus confirming the correctness of the solutions.

Thermal shock induced dynamics of a spacecraft with a flexible deploying boom

NASA Astrophysics Data System (ADS)

Shen, Zhenxing; Li, Huijian; Liu, Xiaoning; Hu, Gengkai

2017-12-01

The dynamics in the process of deployment of a flexible extendible boom as a deployable structure on the spacecraft is studied. For determining the thermally induced vibrations of the boom subjected to an incident solar heat flux, an axially moving thermal-dynamic beam element based on the absolute nodal coordinate formulation which is able to precisely describe the large displacement, rotation and deformation of flexible body is presented. For the elastic forces formulation of variable-length beam element, the enhanced continuum mechanics approach is adopted, which can eliminate the Poisson locking effect, and take into account the tension-bending-torsion coupling deformations. The main body of the spacecraft, modeled as a rigid body, is described using the natural coordinates method. In the derived nonlinear thermal-dynamic equations of rigid-flexible multibody system, the mass matrix is time-variant, and a pseudo damping matrix which is without actual energy dissipation, and a heat conduction matrix which is relative to the moving speed and the number of beam element are arisen. Numerical results give the dynamic and thermal responses of the nonrotating and spinning spacecraft, respectively, and show that thermal shock has a significant influence on the dynamics of spacecraft.

Stochastic modeling for neural spiking events based on fractional superstatistical Poisson process

NASA Astrophysics Data System (ADS)

Konno, Hidetoshi; Tamura, Yoshiyasu

2018-01-01

In neural spike counting experiments, it is known that there are two main features: (i) the counting number has a fractional power-law growth with time and (ii) the waiting time (i.e., the inter-spike-interval) distribution has a heavy tail. The method of superstatistical Poisson processes (SSPPs) is examined whether these main features are properly modeled. Although various mixed/compound Poisson processes are generated with selecting a suitable distribution of the birth-rate of spiking neurons, only the second feature (ii) can be modeled by the method of SSPPs. Namely, the first one (i) associated with the effect of long-memory cannot be modeled properly. Then, it is shown that the two main features can be modeled successfully by a class of fractional SSPP (FSSPP).

Fractional Relativistic Yamaleev Oscillator Model and Its Dynamical Behaviors

NASA Astrophysics Data System (ADS)

Luo, Shao-Kai; He, Jin-Man; Xu, Yan-Li; Zhang, Xiao-Tian

2016-07-01

In the paper we construct a new kind of fractional dynamical model, i.e. the fractional relativistic Yamaleev oscillator model, and explore its dynamical behaviors. We will find that the fractional relativistic Yamaleev oscillator model possesses Lie algebraic structure and satisfies generalized Poisson conservation law. We will also give the Poisson conserved quantities of the model. Further, the relation between conserved quantities and integral invariants of the model is studied and it is proved that, by using the Poisson conserved quantities, we can construct integral invariants of the model. Finally, the stability of the manifold of equilibrium states of the fractional relativistic Yamaleev oscillator model is studied. The paper provides a general method, i.e. fractional generalized Hamiltonian method, for constructing a family of fractional dynamical models of an actual dynamical system.

This is SPIRAL-TAP: Sparse Poisson Intensity Reconstruction ALgorithms--theory and practice.

PubMed

Harmany, Zachary T; Marcia, Roummel F; Willett, Rebecca M

2012-03-01

Observations in many applications consist of counts of discrete events, such as photons hitting a detector, which cannot be effectively modeled using an additive bounded or Gaussian noise model, and instead require a Poisson noise model. As a result, accurate reconstruction of a spatially or temporally distributed phenomenon (f*) from Poisson data (y) cannot be effectively accomplished by minimizing a conventional penalized least-squares objective function. The problem addressed in this paper is the estimation of f* from y in an inverse problem setting, where the number of unknowns may potentially be larger than the number of observations and f* admits sparse approximation. The optimization formulation considered in this paper uses a penalized negative Poisson log-likelihood objective function with nonnegativity constraints (since Poisson intensities are naturally nonnegative). In particular, the proposed approach incorporates key ideas of using separable quadratic approximations to the objective function at each iteration and penalization terms related to l1 norms of coefficient vectors, total variation seminorms, and partition-based multiscale estimation methods.

Vlasov-Maxwell and Vlasov-Poisson equations as models of a one-dimensional electron plasma

NASA Technical Reports Server (NTRS)

Klimas, A. J.; Cooper, J.

1983-01-01

The Vlasov-Maxwell and Vlasov-Poisson systems of equations for a one-dimensional electron plasma are defined and discussed. A method for transforming a solution of one system which is periodic over a bounded or unbounded spatial interval to a similar solution of the other is constructed.

A comparison of different statistical methods analyzing hypoglycemia data using bootstrap simulations.

PubMed

Jiang, Honghua; Ni, Xiao; Huster, William; Heilmann, Cory

2015-01-01

Hypoglycemia has long been recognized as a major barrier to achieving normoglycemia with intensive diabetic therapies. It is a common safety concern for the diabetes patients. Therefore, it is important to apply appropriate statistical methods when analyzing hypoglycemia data. Here, we carried out bootstrap simulations to investigate the performance of the four commonly used statistical models (Poisson, negative binomial, analysis of covariance [ANCOVA], and rank ANCOVA) based on the data from a diabetes clinical trial. Zero-inflated Poisson (ZIP) model and zero-inflated negative binomial (ZINB) model were also evaluated. Simulation results showed that Poisson model inflated type I error, while negative binomial model was overly conservative. However, after adjusting for dispersion, both Poisson and negative binomial models yielded slightly inflated type I errors, which were close to the nominal level and reasonable power. Reasonable control of type I error was associated with ANCOVA model. Rank ANCOVA model was associated with the greatest power and with reasonable control of type I error. Inflated type I error was observed with ZIP and ZINB models.

Determining X-ray source intensity and confidence bounds in crowded fields

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

Primini, F. A.; Kashyap, V. L., E-mail: fap@head.cfa.harvard.edu

We present a rigorous description of the general problem of aperture photometry in high-energy astrophysics photon-count images, in which the statistical noise model is Poisson, not Gaussian. We compute the full posterior probability density function for the expected source intensity for various cases of interest, including the important cases in which both source and background apertures contain contributions from the source, and when multiple source apertures partially overlap. A Bayesian approach offers the advantages of allowing one to (1) include explicit prior information on source intensities, (2) propagate posterior distributions as priors for future observations, and (3) use Poisson likelihoods,more » making the treatment valid in the low-counts regime. Elements of this approach have been implemented in the Chandra Source Catalog.« less

An Intrinsic Algorithm for Parallel Poisson Disk Sampling on Arbitrary Surfaces.

PubMed

Ying, Xiang; Xin, Shi-Qing; Sun, Qian; He, Ying

2013-03-08

Poisson disk sampling plays an important role in a variety of visual computing, due to its useful statistical property in distribution and the absence of aliasing artifacts. While many effective techniques have been proposed to generate Poisson disk distribution in Euclidean space, relatively few work has been reported to the surface counterpart. This paper presents an intrinsic algorithm for parallel Poisson disk sampling on arbitrary surfaces. We propose a new technique for parallelizing the dart throwing. Rather than the conventional approaches that explicitly partition the spatial domain to generate the samples in parallel, our approach assigns each sample candidate a random and unique priority that is unbiased with regard to the distribution. Hence, multiple threads can process the candidates simultaneously and resolve conflicts by checking the given priority values. It is worth noting that our algorithm is accurate as the generated Poisson disks are uniformly and randomly distributed without bias. Our method is intrinsic in that all the computations are based on the intrinsic metric and are independent of the embedding space. This intrinsic feature allows us to generate Poisson disk distributions on arbitrary surfaces. Furthermore, by manipulating the spatially varying density function, we can obtain adaptive sampling easily.

Poisson image reconstruction with Hessian Schatten-norm regularization.

PubMed

Lefkimmiatis, Stamatios; Unser, Michael

2013-11-01

Poisson inverse problems arise in many modern imaging applications, including biomedical and astronomical ones. The main challenge is to obtain an estimate of the underlying image from a set of measurements degraded by a linear operator and further corrupted by Poisson noise. In this paper, we propose an efficient framework for Poisson image reconstruction, under a regularization approach, which depends on matrix-valued regularization operators. In particular, the employed regularizers involve the Hessian as the regularization operator and Schatten matrix norms as the potential functions. For the solution of the problem, we propose two optimization algorithms that are specifically tailored to the Poisson nature of the noise. These algorithms are based on an augmented-Lagrangian formulation of the problem and correspond to two variants of the alternating direction method of multipliers. Further, we derive a link that relates the proximal map of an l(p) norm with the proximal map of a Schatten matrix norm of order p. This link plays a key role in the development of one of the proposed algorithms. Finally, we provide experimental results on natural and biological images for the task of Poisson image deblurring and demonstrate the practical relevance and effectiveness of the proposed framework.

Poisson Approximation-Based Score Test for Detecting Association of Rare Variants.

PubMed

Fang, Hongyan; Zhang, Hong; Yang, Yaning

2016-07-01

Genome-wide association study (GWAS) has achieved great success in identifying genetic variants, but the nature of GWAS has determined its inherent limitations. Under the common disease rare variants (CDRV) hypothesis, the traditional association analysis methods commonly used in GWAS for common variants do not have enough power for detecting rare variants with a limited sample size. As a solution to this problem, pooling rare variants by their functions provides an efficient way for identifying susceptible genes. Rare variant typically have low frequencies of minor alleles, and the distribution of the total number of minor alleles of the rare variants can be approximated by a Poisson distribution. Based on this fact, we propose a new test method, the Poisson Approximation-based Score Test (PAST), for association analysis of rare variants. Two testing methods, namely, ePAST and mPAST, are proposed based on different strategies of pooling rare variants. Simulation results and application to the CRESCENDO cohort data show that our methods are more powerful than the existing methods. © 2016 John Wiley & Sons Ltd/University College London.

A Hierarchical Poisson Log-Normal Model for Network Inference from RNA Sequencing Data

PubMed Central

Gallopin, Mélina; Rau, Andrea; Jaffrézic, Florence

2013-01-01

Gene network inference from transcriptomic data is an important methodological challenge and a key aspect of systems biology. Although several methods have been proposed to infer networks from microarray data, there is a need for inference methods able to model RNA-seq data, which are count-based and highly variable. In this work we propose a hierarchical Poisson log-normal model with a Lasso penalty to infer gene networks from RNA-seq data; this model has the advantage of directly modelling discrete data and accounting for inter-sample variance larger than the sample mean. Using real microRNA-seq data from breast cancer tumors and simulations, we compare this method to a regularized Gaussian graphical model on log-transformed data, and a Poisson log-linear graphical model with a Lasso penalty on power-transformed data. For data simulated with large inter-sample dispersion, the proposed model performs better than the other methods in terms of sensitivity, specificity and area under the ROC curve. These results show the necessity of methods specifically designed for gene network inference from RNA-seq data. PMID:24147011

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

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

Laurence, T; Chromy, B

2009-11-10

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

Leptospirosis disease mapping with standardized morbidity ratio and Poisson-Gamma model: An analysis of Leptospirosis disease in Kelantan, Malaysia

NASA Astrophysics Data System (ADS)

Che Awang, Aznida; Azah Samat, Nor

2017-09-01

Leptospirosis is a disease caused by the infection of pathogenic species from the genus of Leptospira. Human can be infected by the leptospirosis from direct or indirect exposure to the urine of infected animals. The excretion of urine from the animal host that carries pathogenic Leptospira causes the soil or water to be contaminated. Therefore, people can become infected when they are exposed to contaminated soil and water by cut on the skin as well as open wound. It also can enter the human body by mucous membrane such nose, eyes and mouth, for example by splashing contaminated water or urine into the eyes or swallowing contaminated water or food. Currently, there is no vaccine available for the prevention or treatment of leptospirosis disease but this disease can be treated if it is diagnosed early to avoid any complication. The disease risk mapping is important in a way to control and prevention of disease. Using a good choice of statistical model will produce a good disease risk map. Therefore, the aim of this study is to estimate the relative risk for leptospirosis disease based initially on the most common statistic used in disease mapping called Standardized Morbidity Ratio (SMR) and Poisson-gamma model. This paper begins by providing a review of the SMR method and Poisson-gamma model, which we then applied to leptospirosis data of Kelantan, Malaysia. Both results are displayed and compared using graph, tables and maps. The result shows that the second method Poisson-gamma model produces better relative risk estimates compared to the SMR method. This is because the Poisson-gamma model can overcome the drawback of SMR where the relative risk will become zero when there is no observed leptospirosis case in certain regions. However, the Poisson-gamma model also faced problems where the covariate adjustment for this model is difficult and no possibility for allowing spatial correlation between risks in neighbouring areas. The problems of this model have motivated many researchers to introduce other alternative methods for estimating the risk.

[Application of negative binomial regression and modified Poisson regression in the research of risk factors for injury frequency].

PubMed

Cao, Qingqing; Wu, Zhenqiang; Sun, Ying; Wang, Tiezhu; Han, Tengwei; Gu, Chaomei; Sun, Yehuan

2011-11-01

To Eexplore the application of negative binomial regression and modified Poisson regression analysis in analyzing the influential factors for injury frequency and the risk factors leading to the increase of injury frequency. 2917 primary and secondary school students were selected from Hefei by cluster random sampling method and surveyed by questionnaire. The data on the count event-based injuries used to fitted modified Poisson regression and negative binomial regression model. The risk factors incurring the increase of unintentional injury frequency for juvenile students was explored, so as to probe the efficiency of these two models in studying the influential factors for injury frequency. The Poisson model existed over-dispersion (P < 0.0001) based on testing by the Lagrangemultiplier. Therefore, the over-dispersion dispersed data using a modified Poisson regression and negative binomial regression model, was fitted better. respectively. Both showed that male gender, younger age, father working outside of the hometown, the level of the guardian being above junior high school and smoking might be the results of higher injury frequencies. On a tendency of clustered frequency data on injury event, both the modified Poisson regression analysis and negative binomial regression analysis can be used. However, based on our data, the modified Poisson regression fitted better and this model could give a more accurate interpretation of relevant factors affecting the frequency of injury.

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.

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

NASA Astrophysics Data System (ADS)

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

2010-07-01

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

Modeling motor vehicle crashes using Poisson-gamma models: examining the effects of low sample mean values and small sample size on the estimation of the fixed dispersion parameter.

PubMed

Lord, Dominique

2006-07-01

There has been considerable research conducted on the development of statistical models for predicting crashes on highway facilities. Despite numerous advancements made for improving the estimation tools of statistical models, the most common probabilistic structure used for modeling motor vehicle crashes remains the traditional Poisson and Poisson-gamma (or Negative Binomial) distribution; when crash data exhibit over-dispersion, the Poisson-gamma model is usually the model of choice most favored by transportation safety modelers. Crash data collected for safety studies often have the unusual attributes of being characterized by low sample mean values. Studies have shown that the goodness-of-fit of statistical models produced from such datasets can be significantly affected. This issue has been defined as the "low mean problem" (LMP). Despite recent developments on methods to circumvent the LMP and test the goodness-of-fit of models developed using such datasets, no work has so far examined how the LMP affects the fixed dispersion parameter of Poisson-gamma models used for modeling motor vehicle crashes. The dispersion parameter plays an important role in many types of safety studies and should, therefore, be reliably estimated. The primary objective of this research project was to verify whether the LMP affects the estimation of the dispersion parameter and, if it is, to determine the magnitude of the problem. The secondary objective consisted of determining the effects of an unreliably estimated dispersion parameter on common analyses performed in highway safety studies. To accomplish the objectives of the study, a series of Poisson-gamma distributions were simulated using different values describing the mean, the dispersion parameter, and the sample size. Three estimators commonly used by transportation safety modelers for estimating the dispersion parameter of Poisson-gamma models were evaluated: the method of moments, the weighted regression, and the maximum likelihood method. In an attempt to complement the outcome of the simulation study, Poisson-gamma models were fitted to crash data collected in Toronto, Ont. characterized by a low sample mean and small sample size. The study shows that a low sample mean combined with a small sample size can seriously affect the estimation of the dispersion parameter, no matter which estimator is used within the estimation process. The probability the dispersion parameter becomes unreliably estimated increases significantly as the sample mean and sample size decrease. Consequently, the results show that an unreliably estimated dispersion parameter can significantly undermine empirical Bayes (EB) estimates as well as the estimation of confidence intervals for the gamma mean and predicted response. The paper ends with recommendations about minimizing the likelihood of producing Poisson-gamma models with an unreliable dispersion parameter for modeling motor vehicle crashes.

Poisson-Boltzmann model for protein-surface electrostatic interactions and grid-convergence study using the PyGBe code

NASA Astrophysics Data System (ADS)

Cooper, Christopher D.; Barba, Lorena A.

2016-05-01

Interactions between surfaces and proteins occur in many vital processes and are crucial in biotechnology: the ability to control specific interactions is essential in fields like biomaterials, biomedical implants and biosensors. In the latter case, biosensor sensitivity hinges on ligand proteins adsorbing on bioactive surfaces with a favorable orientation, exposing reaction sites to target molecules. Protein adsorption, being a free-energy-driven process, is difficult to study experimentally. This paper develops and evaluates a computational model to study electrostatic interactions of proteins and charged nanosurfaces, via the Poisson-Boltzmann equation. We extended the implicit-solvent model used in the open-source code PyGBe to include surfaces of imposed charge or potential. This code solves the boundary integral formulation of the Poisson-Boltzmann equation, discretized with surface elements. PyGBe has at its core a treecode-accelerated Krylov iterative solver, resulting in O(N log N) scaling, with further acceleration on hardware via multi-threaded execution on GPUs. It computes solvation and surface free energies, providing a framework for studying the effect of electrostatics on adsorption. We derived an analytical solution for a spherical charged surface interacting with a spherical dielectric cavity, and used it in a grid-convergence study to build evidence on the correctness of our approach. The study showed the error decaying with the average area of the boundary elements, i.e., the method is O(1 / N) , which is consistent with our previous verification studies using PyGBe. We also studied grid-convergence using a real molecular geometry (protein G B1 D4‧), in this case using Richardson extrapolation (in the absence of an analytical solution) and confirmed the O(1 / N) scaling. With this work, we can now access a completely new family of problems, which no other major bioelectrostatics solver, e.g. APBS, is capable of dealing with. PyGBe is open-source under an MIT license and is hosted under version control at https://github.com/barbagroup/pygbe. To supplement this paper, we prepared ;reproducibility packages; consisting of running and post-processing scripts in Python for replicating the grid-convergence studies, all the way to generating the final plots, with a single command.

Evaluation of Shiryaev-Roberts Procedure for On-line Environmental Radiation Monitoring

NASA Astrophysics Data System (ADS)

Watson, Mara Mae

An on-line radiation monitoring system that simultaneously concentrates and detects radioactivity is needed to detect an accidental leakage from a nuclear waste disposal facility or clandestine nuclear activity. Previous studies have shown that classical control chart methods can be applied to on-line radiation monitoring data to quickly detect these events as they occur; however, Bayesian control chart methods were not included in these studies. This work will evaluate the performance of a Bayesian control chart method, the Shiryaev-Roberts (SR) procedure, compared to classical control chart methods, Shewhart 3-sigma and cumulative sum (CUSUM), for use in on-line radiation monitoring of 99Tc in water using extractive scintillating resin. Measurements were collected by pumping solutions containing 0.1-5 Bq/L of 99Tc, as 99T cO4-, through a flow cell packed with extractive scintillating resin coupled to a Beta-RAM Model 5 HPLC detector. While 99T cO4- accumulated on the resin, simultaneous measurements were acquired in 10-s intervals and then re-binned to 100-s intervals. The Bayesian statistical method, Shiryaev-Roberts procedure, and classical control chart methods, Shewhart 3-sigma and cumulative sum (CUSUM), were applied to the data using statistical algorithms developed in MATLAB RTM. Two SR control charts were constructed using Poisson distributions and Gaussian distributions to estimate the likelihood ratio, and are referred to as Poisson SR and Gaussian SR to indicate the distribution used to calculate the statistic. The Poisson and Gaussian SR methods required as little as 28.9 mL less solution at 5 Bq/L and as much as 170 mL less solution at 0.5 Bq/L to exceed the control limit than the Shewhart 3-sigma method. The Poisson SR method needed as little as 6.20 mL less solution at 5 Bq/L and up to 125 mL less solution at 0.5 Bq/L to exceed the control limit than the CUSUM method. The Gaussian SR and CUSUM method required comparable solution volumes for test solutions containing at least 1.5 Bq/L of 99T c. For activity concentrations less than 1.5 Bq/L, the Gaussian SR method required as much as 40.8 mL less solution at 0.5 Bq/L to exceed the control limit than the CUSUM method. Both SR methods were able to consistently detect test solutions containing 0.1 Bq/L, unlike the Shewhart 3-sigma and CUSUM methods. Although the Poisson SR method required as much as 178 mL less solution to exceed the control limit than the Gaussian SR method, the Gaussian SR false positive of 0% was much lower than the Poisson SR false positive rate of 1.14%. A lower false positive rate made it easier to differentiate between a false positive and an increase in mean count rate caused by activity accumulating on the resin. The SR procedure is thus the ideal tool for low-level on-line radiation monitoring using extractive scintillating resin, because it needed less volume in most cases to detect an upward shift in the mean count rate than the Shewhart 3-sigma and CUSUM methods and consistently detected lower activity concentrations. The desired results for the monitoring scheme, however, need to be considered prior to choosing between the Poisson and Gaussian distribution to estimate the likelihood ratio, because each was advantageous under different circumstances. Once the control limit was exceeded, activity concentrations were estimated from the SR control chart using the slope of the control chart on a semi-logarithmic plot. Five of nine test solutions for the Poisson SR control chart produced concentration estimates within 30% of the actual value, but the worst case was 263.2% different than the actual value. The estimations for the Gaussian SR control chart were much more precise, with six of eight solutions producing estimates within 30%. Although the activity concentrations estimations were only mediocre for the Poisson SR control chart and satisfactory for the Gaussian SR control chart, these results demonstrate that a relationship exists between activity concentration and the SR control chart magnitude that can be exploited to determine the activity concentration from the SR control chart. More complex methods should be investigated to improve activity concentration estimations from the SR control charts.

Bringing consistency to simulation of population models--Poisson simulation as a bridge between micro and macro simulation.

PubMed

Gustafsson, Leif; Sternad, Mikael

2007-10-01

Population models concern collections of discrete entities such as atoms, cells, humans, animals, etc., where the focus is on the number of entities in a population. Because of the complexity of such models, simulation is usually needed to reproduce their complete dynamic and stochastic behaviour. Two main types of simulation models are used for different purposes, namely micro-simulation models, where each individual is described with its particular attributes and behaviour, and macro-simulation models based on stochastic differential equations, where the population is described in aggregated terms by the number of individuals in different states. Consistency between micro- and macro-models is a crucial but often neglected aspect. This paper demonstrates how the Poisson Simulation technique can be used to produce a population macro-model consistent with the corresponding micro-model. This is accomplished by defining Poisson Simulation in strictly mathematical terms as a series of Poisson processes that generate sequences of Poisson distributions with dynamically varying parameters. The method can be applied to any population model. It provides the unique stochastic and dynamic macro-model consistent with a correct micro-model. The paper also presents a general macro form for stochastic and dynamic population models. In an appendix Poisson Simulation is compared with Markov Simulation showing a number of advantages. Especially aggregation into state variables and aggregation of many events per time-step makes Poisson Simulation orders of magnitude faster than Markov Simulation. Furthermore, you can build and execute much larger and more complicated models with Poisson Simulation than is possible with the Markov approach.

Analytical study of mixed electroosmotic-pressure-driven flow in rectangular micro-channels

NASA Astrophysics Data System (ADS)

Movahed, Saeid; Kamali, Reza; Eghtesad, Mohammad; Khosravifard, Amir

2013-09-01

Operational state of many miniaturized devices deals with flow field in microchannels. Pressure-driven flow (PDF) and electroosmotic flow (EOF) can be recognized as the two most important types of the flow field in such channels. EOF has many advantages in comparison with PDF, such as being vibration free and not requiring any external mechanical pumps or moving parts. However, the disadvantages of this type of flow such as Joule heating, electrophoresis demixing, and not being suitable for mobile devices must be taken into consideration carefully. By using mixed electroosmotic/pressure-driven flow, the role of EOF in producing desired velocity profile will be reduced. In this way, the advantages of EOF can be exploited, and its disadvantages can be prevented. Induced pressure gradient can be utilized in order to control the separation in the system. Furthermore, in many complicated geometries such as T-shape microchannels, turns may induce pressure gradient to the electroosmotic velocity. While analytical formulas are completely essential for analysis and control of any industrial and laboratory microdevices, lack of such formulas in the literature for solving Poisson-Boltzmann equation and predicting electroosmotic velocity field in rectangular domains is evident. In the present study, first a novel method is proposed to solve Poisson-Boltzmann equation (PBE). Subsequently, this solution is utilized to find the electroosmotic and the mixed electroosmotic/pressure-driven velocity profile in a rectangular domain of the microchannels. To demonstrate the accuracy of the presented analytical method in solving PBE and finding electroosmotic velocity, a general nondimensional example is analyzed, and the results are compared with the solution of boundary element method. Additionally, the effects of different nondimensional parameters and also aspect ratio of channels on the electroosmotic part of the flow field will be investigated.

Poisson-Boltzmann versus Size-Modified Poisson-Boltzmann Electrostatics Applied to Lipid Bilayers.

PubMed

Wang, Nuo; Zhou, Shenggao; Kekenes-Huskey, Peter M; Li, Bo; McCammon, J Andrew

2014-12-26

Mean-field methods, such as the Poisson-Boltzmann equation (PBE), are often used to calculate the electrostatic properties of molecular systems. In the past two decades, an enhancement of the PBE, the size-modified Poisson-Boltzmann equation (SMPBE), has been reported. Here, the PBE and the SMPBE are reevaluated for realistic molecular systems, namely, lipid bilayers, under eight different sets of input parameters. The SMPBE appears to reproduce the molecular dynamics simulation results better than the PBE only under specific parameter sets, but in general, it performs no better than the Stern layer correction of the PBE. These results emphasize the need for careful discussions of the accuracy of mean-field calculations on realistic systems with respect to the choice of parameters and call for reconsideration of the cost-efficiency and the significance of the current SMPBE formulation.

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

Equivalence of MAXENT and Poisson point process models for species distribution modeling in ecology.

PubMed

Renner, Ian W; Warton, David I

2013-03-01

Modeling the spatial distribution of a species is a fundamental problem in ecology. A number of modeling methods have been developed, an extremely popular one being MAXENT, a maximum entropy modeling approach. In this article, we show that MAXENT is equivalent to a Poisson regression model and hence is related to a Poisson point process model, differing only in the intercept term, which is scale-dependent in MAXENT. We illustrate a number of improvements to MAXENT that follow from these relations. In particular, a point process model approach facilitates methods for choosing the appropriate spatial resolution, assessing model adequacy, and choosing the LASSO penalty parameter, all currently unavailable to MAXENT. The equivalence result represents a significant step in the unification of the species distribution modeling literature. Copyright © 2013, The International Biometric Society.

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

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 new method for extracting near-surface mass-density anomalies from land-based gravity data, based on a special case of Poisson's PDE at the Earth's surface: A case study of salt diapirs in the south of Iran

NASA Astrophysics Data System (ADS)

AllahTavakoli, Y.; Safari, A.; Ardalan, A.; Bahroudi, A.

2015-12-01

The current research provides a method for tracking near-surface mass-density anomalies via using only land-based gravity data, which is based on a special version of Poisson's Partial Differential Equation (PDE) of the gravitational field at Earth's surface. The research demonstrates how the Poisson's PDE can provide us with a capability to extract the near-surface mass-density anomalies from land-based gravity data. Herein, this version of the Poisson's PDE is mathematically introduced to the Earth's surface and then it is used to develop the new method for approximating the mass-density via derivatives of the Earth's gravitational field (i.e. via the gradient tensor). Herein, the author believes that the PDE can give us new knowledge about the behavior of the Earth's gravitational field at the Earth's surface which can be so useful for developing new methods of Earth's mass-density determination. In a case study, the proposed method is applied to a set of gravity stations located in the south of Iran. The results were numerically validated via certain knowledge about the geological structures in the area of the case study. Also, the method was compared with two standard methods of mass-density determination. All the numerical experiments show that the proposed approach is well-suited for tracking near-surface mass-density anomalies via using only the gravity data. Finally, the approach is also applied to some petroleum exploration studies of salt diapirs in the south of Iran.

The classical dynamic symmetry for the U(1) -Kepler problems

NASA Astrophysics Data System (ADS)

Bouarroudj, Sofiane; Meng, Guowu

2018-01-01

For the Jordan algebra of hermitian matrices of order n ≥ 2, we let X be its submanifold consisting of rank-one semi-positive definite elements. The composition of the cotangent bundle map πX: T∗ X → X with the canonical map X → CP n - 1 (i.e., the map that sends a given hermitian matrix to its column space), pulls back the Kähler form of the Fubini-Study metric on CP n - 1 to a real closed differential two-form ωK on T∗ X. Let ωX be the canonical symplectic form on T∗ X and μ a real number. A standard fact says that ωμ ≔ωX + 2 μωK turns T∗ X into a symplectic manifold, hence a Poisson manifold with Poisson bracket {,}μ. In this article we exhibit a Poisson realization of the simple real Lie algebra su(n , n) on the Poisson manifold (T∗ X ,{,}μ) , i.e., a Lie algebra homomorphism from su(n , n) to (C∞(T∗ X , R) ,{,}μ). Consequently one obtains the Laplace-Runge-Lenz vector for the classical U(1) -Kepler problem of level n and magnetic charge μ. Since the McIntosh-Cisneros-Zwanziger-Kepler problems (MICZ-Kepler Problems) are the U(1) -Kepler problems of level 2, the work presented here is a direct generalization of the work by A. Barut and G. Bornzin (1971) on the classical dynamic symmetry for the MICZ-Kepler problems.

A free energy satisfying discontinuous Galerkin method for one-dimensional Poisson-Nernst-Planck systems

NASA Astrophysics Data System (ADS)

Liu, Hailiang; Wang, Zhongming

2017-01-01

We design an arbitrary-order free energy satisfying discontinuous Galerkin (DG) method for solving time-dependent Poisson-Nernst-Planck systems. Both the semi-discrete and fully discrete DG methods are shown to satisfy the corresponding discrete free energy dissipation law for positive numerical solutions. Positivity of numerical solutions is enforced by an accuracy-preserving limiter in reference to positive cell averages. Numerical examples are presented to demonstrate the high resolution of the numerical algorithm and to illustrate the proven properties of mass conservation, free energy dissipation, as well as the preservation of steady states.

Direct Coupling Method for Time-Accurate Solution of Incompressible Navier-Stokes Equations

NASA Technical Reports Server (NTRS)

Soh, Woo Y.

1992-01-01

A noniterative finite difference numerical method is presented for the solution of the incompressible Navier-Stokes equations with second order accuracy in time and space. Explicit treatment of convection and diffusion terms and implicit treatment of the pressure gradient give a single pressure Poisson equation when the discretized momentum and continuity equations are combined. A pressure boundary condition is not needed on solid boundaries in the staggered mesh system. The solution of the pressure Poisson equation is obtained directly by Gaussian elimination. This method is tested on flow problems in a driven cavity and a curved duct.

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.

Data precision of X-ray fluorescence (XRF) scanning of discrete samples with the ITRAX XRF core-scanner exemplified on loess-paleosol samples

NASA Astrophysics Data System (ADS)

Profe, Jörn; Ohlendorf, Christian

2017-04-01

XRF-scanning is the state-of-the-art technique for geochemical analyses in marine and lacustrine sedimentology for more than a decade. However, little attention has been paid to data precision and technical limitations so far. Using homogenized, dried and powdered samples (certified geochemical reference standards and samples from a lithologically-contrasting loess-paleosol sequence) minimizes many adverse effects that influence the XRF-signal when analyzing wet sediment cores. This allows the investigation of data precision under ideal conditions and documents a new application of the XRF core-scanner technology at the same time. Reliable interpretations of XRF results require data precision evaluation of single elements as a function of X-ray tube, measurement time, sample compaction and quality of peak fitting. Ten-fold measurement of each sample constitutes data precision. Data precision of XRF measurements theoretically obeys Poisson statistics. Fe and Ca exhibit largest deviations from Poisson statistics. The same elements show the least mean relative standard deviations in the range from 0.5% to 1%. This represents the technical limit of data precision achievable by the installed detector. Measurement times ≥ 30 s reveal mean relative standard deviations below 4% for most elements. The quality of peak fitting is only relevant for elements with overlapping fluorescence lines such as Ba, Ti and Mn or for elements with low concentrations such as Y, for example. Differences in sample compaction are marginal and do not change mean relative standard deviation considerably. Data precision is in the range reported for geochemical reference standards measured by conventional techniques. Therefore, XRF scanning of discrete samples provide a cost- and time-efficient alternative to conventional multi-element analyses. As best trade-off between economical operation and data quality, we recommend a measurement time of 30 s resulting in a total scan time of 30 minutes for 30 samples.

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

Efficient Charge Collection in Coplanar-Grid Radiation Detectors

NASA Astrophysics Data System (ADS)

Kunc, J.; Praus, P.; Belas, E.; Dědič, V.; Pekárek, J.; Grill, R.

2018-05-01

We model laser-induced transient-current waveforms in radiation coplanar-grid detectors. Poisson's equation is solved by the finite-element method and currents induced by a photogenerated charge are obtained using the Shockley-Ramo theorem. The spectral response on a radiation flux is modeled by Monte Carlo simulations. We show a 10 × improved spectral resolution of the coplanar-grid detector using differential signal sensing. We model the current waveform dependence on the doping, depletion width, diffusion, and detector shielding, and their mutual dependence is discussed in terms of detector optimization. The numerical simulations are successfully compared to experimental data, and further model simplifications are proposed. The space charge below electrodes and a nonhomogeneous electric field on a coplanar-grid anode are found to be the dominant contributions to laser-induced transient-current waveforms.

Modeling of electrically actuated elastomer structures for electro-optical modulation

NASA Astrophysics Data System (ADS)

Kluge, Christian; Galler, Nicole; Ditlbacher, Harald; Gerken, Martina

2011-02-01

A transparent elastomer layer sandwiched between two metal electrodes deforms upon voltage application due to electrostatic forces. This structure can be used as tunable waveguide. We investigate structures of a polydimethylsiloxane (PDMS) layer with 1-30 μm thickness and 40 nm gold electrodes. For extended electrodes the effect size may be calculated analytically as a function of the Poisson ratio. A fully coupled finite-element method (FEM) is used for calculation of the position-dependent deformation in case of structured electrodes. Different geometries are compared concerning actuation effect size and homogeneity. Structuring of the top electrode results in high effect magnitude, but non-uniform deformation concentrated at the electrode edges. Structured bottom electrodes provide good compromise between effect size and homogeneity for electrode widths of 2.75 times the elastomer thickness.

Species abundance in a forest community in South China: A case of poisson lognormal distribution

USGS Publications Warehouse

Yin, Z.-Y.; Ren, H.; Zhang, Q.-M.; Peng, S.-L.; Guo, Q.-F.; Zhou, G.-Y.

2005-01-01

Case studies on Poisson lognormal distribution of species abundance have been rare, especially in forest communities. We propose a numerical method to fit the Poisson lognormal to the species abundance data at an evergreen mixed forest in the Dinghushan Biosphere Reserve, South China. Plants in the tree, shrub and herb layers in 25 quadrats of 20 m??20 m, 5 m??5 m, and 1 m??1 m were surveyed. Results indicated that: (i) for each layer, the observed species abundance with a similarly small median, mode, and a variance larger than the mean was reverse J-shaped and followed well the zero-truncated Poisson lognormal; (ii) the coefficient of variation, skewness and kurtosis of abundance, and two Poisson lognormal parameters (?? and ??) for shrub layer were closer to those for the herb layer than those for the tree layer; and (iii) from the tree to the shrub to the herb layer, the ?? and the coefficient of variation decreased, whereas diversity increased. We suggest that: (i) the species abundance distributions in the three layers reflects the overall community characteristics; (ii) the Poisson lognormal can describe the species abundance distribution in diverse communities with a few abundant species but many rare species; and (iii) 1/?? should be an alternative measure of diversity.

Reversible dilatancy in entangled single-wire materials.

PubMed

Rodney, David; Gadot, Benjamin; Martinez, Oriol Riu; du Roscoat, Sabine Rolland; Orgéas, Laurent

2016-01-01

Designing structures that dilate rapidly in both tension and compression would benefit devices such as smart filters, actuators or fasteners. This property however requires an unusual Poisson ratio, or Poisson function at finite strains, which has to vary with applied strain and exceed the familiar bounds: less than 0 in tension and above 1/2 in compression. Here, by combining mechanical tests and discrete element simulations, we show that a simple three-dimensional architected material, made of a self-entangled single long coiled wire, behaves in between discrete and continuum media, with a large and reversible dilatancy in both tension and compression. This unusual behaviour arises from an interplay between the elongation of the coiled wire and rearrangements due to steric effects, which, unlike in traditional discrete media, are hysteretically reversible when the architecture is made of an elastic fibre.

Six-component semi-discrete integrable nonlinear Schrödinger system

NASA Astrophysics Data System (ADS)

Vakhnenko, Oleksiy O.

2018-01-01

We suggest the six-component integrable nonlinear system on a quasi-one-dimensional lattice. Due to its symmetrical form, the general system permits a number of reductions; one of which treated as the semi-discrete integrable nonlinear Schrödinger system on a lattice with three structural elements in the unit cell is considered in considerable details. Besides six truly independent basic field variables, the system is characterized by four concomitant fields whose background values produce three additional types of inter-site resonant interactions between the basic fields. As a result, the system dynamics becomes associated with the highly nonstandard form of Poisson structure. The elementary Poisson brackets between all field variables are calculated and presented explicitly. The richness of system dynamics is demonstrated on the multi-component soliton solution written in terms of properly parameterized soliton characteristics.

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.

The Electric Potential of a Macromolecule in a Solvent: A Fundamental Approach

NASA Astrophysics Data System (ADS)

Juffer, André H.; Botta, Eugen F. F.; van Keulen, Bert A. M.; van der Ploeg, Auke; Berendsen, Herman J. C.

1991-11-01

A general numerical method is presented to compute the electric potential for a macromolecule of arbitrary shape in a solvent with nonzero ionic strength. The model is based on a continuum description of the dielectric and screening properties of the system, which consists of a bounded internal region with discrete charges and an infinite external region. The potential obeys the Poisson equation in the internal region and the linearized Poisson-Boltzmann equation in the external region, coupled through appropriate boundary conditions. It is shown how this three-dimensional problem can be presented as a pair of coupled integral equations for the potential and the normal component of the electric field at the dielectric interface. These equations can be solved by a straightforward application of boundary element techniques. The solution involves the decomposition of a matrix that depends only on the geometry of the surface and not on the positions of the charges. With this approach the number of unknowns is reduced by an order of magnitude with respect to the usual finite difference methods. Special attention is given to the numerical inaccuracies resulting from charges which are located close to the interface; an adapted formulation is given for that case. The method is tested both for a spherical geometry, for which an exact solution is available, and for a realistic problem, for which a finite difference solution and experimental verification is available. The latter concerns the shift in acid strength (pK-values) of histidines in the copper-containing protein azurin on oxidation of the copper, for various values of the ionic strength. A general method is given to triangulate a macromolecular surface. The possibility is discussed to use the method presented here for a correct treatment of long-range electrostatic interactions in simulations of solvated macromolecules, which form an essential part of correct potentials of mean force.

Validation of the Poisson Stochastic Radiative Transfer Model

NASA Technical Reports Server (NTRS)

Zhuravleva, Tatiana; Marshak, Alexander

2004-01-01

A new approach to validation of the Poisson stochastic radiative transfer method is proposed. In contrast to other validations of stochastic models, the main parameter of the Poisson model responsible for cloud geometrical structure - cloud aspect ratio - is determined entirely by matching measurements and calculations of the direct solar radiation. If the measurements of the direct solar radiation is unavailable, it was shown that there is a range of the aspect ratios that allows the stochastic model to accurately approximate the average measurements of surface downward and cloud top upward fluxes. Realizations of the fractionally integrated cascade model are taken as a prototype of real measurements.

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

NASA Astrophysics Data System (ADS)

Zhu, Jian T.

1991-12-01

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

Prediction of forest fires occurrences with area-level Poisson mixed models.

PubMed

Boubeta, Miguel; Lombardía, María José; Marey-Pérez, Manuel Francisco; Morales, Domingo

2015-05-01

The number of fires in forest areas of Galicia (north-west of Spain) during the summer period is quite high. Local authorities are interested in analyzing the factors that explain this phenomenon. Poisson regression models are good tools for describing and predicting the number of fires per forest areas. This work employs area-level Poisson mixed models for treating real data about fires in forest areas. A parametric bootstrap method is applied for estimating the mean squared errors of fires predictors. The developed methodology and software are applied to a real data set of fires in forest areas of Galicia. Copyright © 2015 Elsevier Ltd. All rights reserved.

A spectral Poisson solver for kinetic plasma simulation

NASA Astrophysics Data System (ADS)

Szeremley, Daniel; Obberath, Jens; Brinkmann, Ralf

2011-10-01

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

in Mapping of Gastric Cancer Incidence in Iran

PubMed

Asmarian, Naeimehossadat; Jafari-Koshki, Tohid; Soleimani, Ali; Taghi Ayatollahi, Seyyed Mohammad

2016-10-01

Background: In many countries gastric cancer has the highest incidence among the gastrointestinal cancers and is the second most common cancer in Iran. The aim of this study was to identify and map high risk gastric cancer regions at the county-level in Iran. Methods: In this study we analyzed gastric cancer data for Iran in the years 2003-2010. Areato- area Poisson kriging and Besag, York and Mollie (BYM) spatial models were applied to smoothing the standardized incidence ratios of gastric cancer for the 373 counties surveyed in this study. The two methods were compared in term of accuracy and precision in identifying high risk regions. Result: The highest smoothed standardized incidence rate (SIR) according to area-to-area Poisson kriging was in Meshkinshahr county in Ardabil province in north-western Iran (2.4,SD=0.05), while the highest smoothed standardized incidence rate (SIR) according to the BYM model was in Ardabil, the capital of that province (2.9,SD=0.09). Conclusion: Both methods of mapping, ATA Poisson kriging and BYM, showed the gastric cancer incidence rate to be highest in north and north-west Iran. However, area-to-area Poisson kriging was more precise than the BYM model and required less smoothing. According to the results obtained, preventive measures and treatment programs should be focused on particular counties of Iran. Creative Commons Attribution License

New method for blowup of the Euler-Poisson system

NASA Astrophysics Data System (ADS)

Kwong, Man Kam; Yuen, Manwai

2016-08-01

In this paper, we provide a new method for establishing the blowup of C2 solutions for the pressureless Euler-Poisson system with attractive forces for RN (N ≥ 2) with ρ(0, x0) > 0 and Ω 0 i j ( x 0 ) = /1 2 [" separators=" ∂ i u j ( 0 , x 0 ) - ∂ j u i ( 0 , x 0 ) ] = 0 at some point x0 ∈ RN. By applying the generalized Hubble transformation div u ( t , x 0 ( t ) ) = /N a ˙ ( t ) a ( t ) to a reduced Riccati differential inequality derived from the system, we simplify the inequality into the Emden equation a ̈ ( t ) = - /λ a ( t ) N - 1 , a ( 0 ) = 1 , a ˙ ( 0 ) = /div u ( 0 , x 0 ) N . Known results on its blowup set allow us to easily obtain the blowup conditions of the Euler-Poisson system.

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.

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.

Using Response Surface Methods to Correlate the Modal Test of an Inflatable Test Article

NASA Technical Reports Server (NTRS)

Gupta, Anju

2013-01-01

This paper presents a practical application of response surface methods (RSM) to correlate a finite element model of a structural modal test. The test article is a quasi-cylindrical inflatable structure which primarily consists of a fabric weave, with an internal bladder and metallic bulkheads on either end. To mitigate model size, the fabric weave was simplified by representing it with shell elements. The task at hand is to represent the material behavior of the weave. The success of the model correlation is measured by comparing the four major modal frequencies of the analysis model to the four major modal frequencies of the test article. Given that only individual strap material properties were provided and material properties of the overall weave were not available, defining the material properties of the finite element model became very complex. First it was necessary to determine which material properties (modulus of elasticity in the hoop and longitudinal directions, shear modulus, Poisson's ratio, etc.) affected the modal frequencies. Then a Latin Hypercube of the parameter space was created to form an efficiently distributed finite case set. Each case was then analyzed with the results input into RSM. In the resulting response surface it was possible to see how each material parameter affected the modal frequencies of the analysis model. If the modal frequencies of the analysis model and its corresponding parameters match the test with acceptable accuracy, it can be said that the model correlation is successful.

Maslov indices, Poisson brackets, and singular differential forms

NASA Astrophysics Data System (ADS)

Esterlis, I.; Haggard, H. M.; Hedeman, A.; Littlejohn, R. G.

2014-06-01

Maslov indices are integers that appear in semiclassical wave functions and quantization conditions. They are often notoriously difficult to compute. We present methods of computing the Maslov index that rely only on typically elementary Poisson brackets and simple linear algebra. We also present a singular differential form, whose integral along a curve gives the Maslov index of that curve. The form is closed but not exact, and transforms by an exact differential under canonical transformations. We illustrate the method with the 6j-symbol, which is important in angular-momentum theory and in quantum gravity.

Evaluation of Strip Footing Bearing Capacity Built on the Anthropogenic Embankment by Random Finite Element Method

NASA Astrophysics Data System (ADS)

Pieczynska-Kozlowska, Joanna

2014-05-01

One of a geotechnical problem in the area of Wroclaw is an anthropogenic embankment layer delaying to the depth of 4-5m, arising as a result of historical incidents. In such a case an assumption of bearing capacity of strip footing might be difficult. The standard solution is to use a deep foundation or foundation soil replacement. However both methods generate significant costs. In the present paper the authors focused their attention on the influence of anthropogenic embankment variability on bearing capacity. Soil parameters were defined on the basis of CPT test and modeled as 2D anisotropic random fields and the assumption of bearing capacity were made according deterministic finite element methods. Many repeated of the different realizations of random fields lead to stable expected value of bearing capacity. The algorithm used to estimate the bearing capacity of strip footing was the random finite element method (e.g. [1]). In traditional approach of bearing capacity the formula proposed by [2] is taken into account. qf = c'Nc + qNq + 0.5γBN- γ (1) where: qf is the ultimate bearing stress, cis the cohesion, qis the overburden load due to foundation embedment, γ is the soil unit weight, Bis the footing width, and Nc, Nq and Nγ are the bearing capacity factors. The method of evaluation the bearing capacity of strip footing based on finite element method incorporate five parameters: Young's modulus (E), Poisson's ratio (ν), dilation angle (ψ), cohesion (c), and friction angle (φ). In the present study E, ν and ψ are held constant while c and φ are randomized. Although the Young's modulus does not affect the bearing capacity it governs the initial elastic response of the soil. Plastic stress redistribution is accomplished using a viscoplastic algorithm merge with an elastic perfectly plastic (Mohr - Coulomb) failure criterion. In this paper a typical finite element mesh was assumed with 8-node elements consist in 50 columns and 20 rows. Footings width B occupies 10 elements, 0.1 x 0.1 meter size. The footings are placed at the center of the mesh. Figure 1 shows the mesh used in probabilistic bearing capacity analysis. PIC Figure 1- Mesh used in analyses REFERENCES Fenton, G.A., Griffiths, D.V., (2008) Risk Assessment in Geotechnical Engineering, John Wiley & Sons, New York, Terzaghi, K. (1943). Theoretical Soil Mechanics, New York: John Wiley & Sons.

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

PubMed Central

Zhang, Tingting; Kou, S. C.

2010-01-01

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

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

PubMed

Zhang, Tingting; Kou, S C

2010-01-01

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

Object-oriented design and implementation of CFDLab: a computer-assisted learning tool for fluid dynamics using dual reciprocity boundary element methodology

NASA Astrophysics Data System (ADS)

Friedrich, J.

1999-08-01

As lecturers, our main concern and goal is to develop more attractive and efficient ways of communicating up-to-date scientific knowledge to our students and facilitate an in-depth understanding of physical phenomena. Computer-based instruction is very promising to help both teachers and learners in their difficult task, which involves complex cognitive psychological processes. This complexity is reflected in high demands on the design and implementation methods used to create computer-assisted learning (CAL) programs. Due to their concepts, flexibility, maintainability and extended library resources, object-oriented modeling techniques are very suitable to produce this type of pedagogical tool. Computational fluid dynamics (CFD) enjoys not only a growing importance in today's research, but is also very powerful for teaching and learning fluid dynamics. For this purpose, an educational PC program for university level called 'CFDLab 1.1' for Windows™ was developed with an interactive graphical user interface (GUI) for multitasking and point-and-click operations. It uses the dual reciprocity boundary element method as a versatile numerical scheme, allowing to handle a variety of relevant governing equations in two dimensions on personal computers due to its simple pre- and postprocessing including 2D Laplace, Poisson, diffusion, transient convection-diffusion.

Numerical investigation of shape domain effect to its elasticity and surface energy using adaptive finite element method

NASA Astrophysics Data System (ADS)

Alfat, Sayahdin; Kimura, Masato; Firihu, Muhammad Zamrun; Rahmat

2018-05-01

In engineering area, investigation of shape effect in elastic materials was very important. It can lead changing elasticity and surface energy, and also increase of crack propagation in the material. A two-dimensional mathematical model was developed to investigation of elasticity and surface energy in elastic material by Adaptive Finite Element Method. Besides that, behavior of crack propagation has observed for every those materials. The government equations were based on a phase field approach in crack propagation model that developed by Takaishi-Kimura. This research has varied four shape domains where physical properties of materials were same (Young's modulus E = 70 GPa and Poisson's ratio ν = 0.334). Investigation assumptions were; (1) homogeneous and isotropic material, (2) there was not initial cracking at t = 0, (3) initial displacement was zero [u1, u2] = 0) at initial condition (t = 0), and (4) length of time simulation t = 5 with interval Δt = 0.005. Mode I/II or mixed mode crack propagation has been used for the numerical investigation. Results of this studies were very good and accurate to show changing energy and behavior of crack propagation. In the future time, this research can be developed to complex phenomena and domain. Furthermore, shape optimization can be investigation by the model.

Coupling of a structural analysis and flow simulation for short-fiber-reinforced polymers: property prediction and transfer of results

NASA Astrophysics Data System (ADS)

Kröner, C.; Altenbach, H.; Naumenko, K.

2009-05-01

The aim of this paper is to discuss the basic theories of interfaces able to transfer the results of an injection molding analyis of fiber-reinforced polymers, performed by using the commercial computer code Moldflow, to the structural analysis program ABAQUS. The elastic constants of the materials, such as Young's modulus, shear modulus, and Poisson's ratio, which depend on both the fiber content and the degree of fiber orientation, were calculated not by the usual method of "orientation averaging," but with the help of linear functions fitted to experimental data. The calculation and transfer of all needed data, such as material properties, geometry, directions of anisotropy, and so on, is performed by an interface developed. The interface is suit able for midplane elements in Moldflow. It calculates and transfers to ABAQUS all data necessary for the use of shell elements. In addition, a method is described how a nonlinear orthotropic behavior can be modeled starting from the generalized Hooke's law. It is also shown how such a model can be implemented in ABAQUS by means of a material subroutine. The results obtained according to this subroutine are compared with those based on an orthotropic, linear, elastic simulation.

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

The analysis of incontinence episodes and other count data in patients with overactive bladder by Poisson and negative binomial regression.

PubMed

Martina, R; Kay, R; van Maanen, R; Ridder, A

2015-01-01

Clinical studies in overactive bladder have traditionally used analysis of covariance or nonparametric methods to analyse the number of incontinence episodes and other count data. It is known that if the underlying distributional assumptions of a particular parametric method do not hold, an alternative parametric method may be more efficient than a nonparametric one, which makes no assumptions regarding the underlying distribution of the data. Therefore, there are advantages in using methods based on the Poisson distribution or extensions of that method, which incorporate specific features that provide a modelling framework for count data. One challenge with count data is overdispersion, but methods are available that can account for this through the introduction of random effect terms in the modelling, and it is this modelling framework that leads to the negative binomial distribution. These models can also provide clinicians with a clearer and more appropriate interpretation of treatment effects in terms of rate ratios. In this paper, the previously used parametric and non-parametric approaches are contrasted with those based on Poisson regression and various extensions in trials evaluating solifenacin and mirabegron in patients with overactive bladder. In these applications, negative binomial models are seen to fit the data well. Copyright © 2014 John Wiley & Sons, Ltd.

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

NASA Astrophysics Data System (ADS)

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

2017-11-01

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

A Legendre–Fourier spectral method with exact conservation laws for the Vlasov–Poisson system

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

Manzini, Gianmarco; Delzanno, Gian Luca; Vencels, Juris

In this study, we present the design and implementation of an L 2-stable spectral method for the discretization of the Vlasov–Poisson model of a collisionless plasma in one space and velocity dimension. The velocity and space dependence of the Vlasov equation are resolved through a truncated spectral expansion based on Legendre and Fourier basis functions, respectively. The Poisson equation, which is coupled to the Vlasov equation, is also resolved through a Fourier expansion. The resulting system of ordinary differential equation is discretized by the implicit second-order accurate Crank–Nicolson time discretization. The non-linear dependence between the Vlasov and Poisson equations ismore » iteratively solved at any time cycle by a Jacobian-Free Newton–Krylov method. In this work we analyze the structure of the main conservation laws of the resulting Legendre–Fourier model, e.g., mass, momentum, and energy, and prove that they are exactly satisfied in the semi-discrete and discrete setting. The L 2-stability of the method is ensured by discretizing the boundary conditions of the distribution function at the boundaries of the velocity domain by a suitable penalty term. The impact of the penalty term on the conservation properties is investigated theoretically and numerically. An implementation of the penalty term that does not affect the conservation of mass, momentum and energy, is also proposed and studied. A collisional term is introduced in the discrete model to control the filamentation effect, but does not affect the conservation properties of the system. Numerical results on a set of standard test problems illustrate the performance of the method.« less

A Legendre–Fourier spectral method with exact conservation laws for the Vlasov–Poisson system

DOE PAGES

Manzini, Gianmarco; Delzanno, Gian Luca; Vencels, Juris; ...

2016-04-22

In this study, we present the design and implementation of an L 2-stable spectral method for the discretization of the Vlasov–Poisson model of a collisionless plasma in one space and velocity dimension. The velocity and space dependence of the Vlasov equation are resolved through a truncated spectral expansion based on Legendre and Fourier basis functions, respectively. The Poisson equation, which is coupled to the Vlasov equation, is also resolved through a Fourier expansion. The resulting system of ordinary differential equation is discretized by the implicit second-order accurate Crank–Nicolson time discretization. The non-linear dependence between the Vlasov and Poisson equations ismore » iteratively solved at any time cycle by a Jacobian-Free Newton–Krylov method. In this work we analyze the structure of the main conservation laws of the resulting Legendre–Fourier model, e.g., mass, momentum, and energy, and prove that they are exactly satisfied in the semi-discrete and discrete setting. The L 2-stability of the method is ensured by discretizing the boundary conditions of the distribution function at the boundaries of the velocity domain by a suitable penalty term. The impact of the penalty term on the conservation properties is investigated theoretically and numerically. An implementation of the penalty term that does not affect the conservation of mass, momentum and energy, is also proposed and studied. A collisional term is introduced in the discrete model to control the filamentation effect, but does not affect the conservation properties of the system. Numerical results on a set of standard test problems illustrate the performance of the method.« less

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

PubMed Central

Reich, Steven

2014-01-01

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

NEWTPOIS- NEWTON POISSON DISTRIBUTION PROGRAM

NASA Technical Reports Server (NTRS)

Bowerman, P. N.

1994-01-01

The cumulative poisson distribution program, NEWTPOIS, is one of two programs which make calculations involving cumulative poisson distributions. Both programs, NEWTPOIS (NPO-17715) and CUMPOIS (NPO-17714), can be used independently of one another. NEWTPOIS determines percentiles for gamma distributions with integer shape parameters and calculates percentiles for chi-square distributions with even degrees of freedom. It can be used by statisticians and others concerned with probabilities of independent events occurring over specific units of time, area, or volume. NEWTPOIS determines the Poisson parameter (lambda), that is; the mean (or expected) number of events occurring in a given unit of time, area, or space. Given that the user already knows the cumulative probability for a specific number of occurrences (n) it is usually a simple matter of substitution into the Poisson distribution summation to arrive at lambda. However, direct calculation of the Poisson parameter becomes difficult for small positive values of n and unmanageable for large values. NEWTPOIS uses Newton's iteration method to extract lambda from the initial value condition of the Poisson distribution where n=0, taking successive estimations until some user specified error term (epsilon) is reached. The NEWTPOIS program is written in C. It was developed on an IBM AT with a numeric co-processor using Microsoft C 5.0. Because the source code is written using standard C structures and functions, it should compile correctly on most C compilers. The program format is interactive, accepting epsilon, n, and the cumulative probability of the occurrence of n as inputs. It has been implemented under DOS 3.2 and has a memory requirement of 30K. NEWTPOIS was developed in 1988.

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

NASA Technical Reports Server (NTRS)

Chan, Tony F.; Fatoohi, Rod A.

1990-01-01

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

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.

A biomolecular electrostatics solver using Python, GPUs and boundary elements that can handle solvent-filled cavities and Stern layers.

PubMed

Cooper, Christopher D; Bardhan, Jaydeep P; Barba, L A

2014-03-01

The continuum theory applied to biomolecular electrostatics leads to an implicit-solvent model governed by the Poisson-Boltzmann equation. Solvers relying on a boundary integral representation typically do not consider features like solvent-filled cavities or ion-exclusion (Stern) layers, due to the added difficulty of treating multiple boundary surfaces. This has hindered meaningful comparisons with volume-based methods, and the effects on accuracy of including these features has remained unknown. This work presents a solver called PyGBe that uses a boundary-element formulation and can handle multiple interacting surfaces. It was used to study the effects of solvent-filled cavities and Stern layers on the accuracy of calculating solvation energy and binding energy of proteins, using the well-known apbs finite-difference code for comparison. The results suggest that if required accuracy for an application allows errors larger than about 2% in solvation energy, then the simpler, single-surface model can be used. When calculating binding energies, the need for a multi-surface model is problem-dependent, becoming more critical when ligand and receptor are of comparable size. Comparing with the apbs solver, the boundary-element solver is faster when the accuracy requirements are higher. The cross-over point for the PyGBe code is in the order of 1-2% error, when running on one gpu card (nvidia Tesla C2075), compared with apbs running on six Intel Xeon cpu cores. PyGBe achieves algorithmic acceleration of the boundary element method using a treecode, and hardware acceleration using gpus via PyCuda from a user-visible code that is all Python. The code is open-source under MIT license.

A biomolecular electrostatics solver using Python, GPUs and boundary elements that can handle solvent-filled cavities and Stern layers

NASA Astrophysics Data System (ADS)

Cooper, Christopher D.; Bardhan, Jaydeep P.; Barba, L. A.

2014-03-01

The continuum theory applied to biomolecular electrostatics leads to an implicit-solvent model governed by the Poisson-Boltzmann equation. Solvers relying on a boundary integral representation typically do not consider features like solvent-filled cavities or ion-exclusion (Stern) layers, due to the added difficulty of treating multiple boundary surfaces. This has hindered meaningful comparisons with volume-based methods, and the effects on accuracy of including these features has remained unknown. This work presents a solver called PyGBe that uses a boundary-element formulation and can handle multiple interacting surfaces. It was used to study the effects of solvent-filled cavities and Stern layers on the accuracy of calculating solvation energy and binding energy of proteins, using the well-known APBS finite-difference code for comparison. The results suggest that if required accuracy for an application allows errors larger than about 2% in solvation energy, then the simpler, single-surface model can be used. When calculating binding energies, the need for a multi-surface model is problem-dependent, becoming more critical when ligand and receptor are of comparable size. Comparing with the APBS solver, the boundary-element solver is faster when the accuracy requirements are higher. The cross-over point for the PyGBe code is on the order of 1-2% error, when running on one GPU card (NVIDIA Tesla C2075), compared with APBS running on six Intel Xeon CPU cores. PyGBe achieves algorithmic acceleration of the boundary element method using a treecode, and hardware acceleration using GPUs via PyCuda from a user-visible code that is all Python. The code is open-source under MIT license.

Stability of Poisson Equilibria and Hamiltonian Relative Equilibria by Energy Methods

NASA Astrophysics Data System (ADS)

Patrick, George W.; Roberts, Mark; Wulff, Claudia

2004-12-01

We develop a general stability theory for equilibrium points of Poisson dynamical systems and relative equilibria of Hamiltonian systems with symmetries, including several generalisations of the Energy-Casimir and Energy-Momentum Methods. Using a topological generalisation of Lyapunov’s result that an extremal critical point of a conserved quantity is stable, we show that a Poisson equilibrium is stable if it is an isolated point in the intersection of a level set of a conserved function with a subset of the phase space that is related to the topology of the symplectic leaf space at that point. This criterion is applied to generalise the energy-momentum method to Hamiltonian systems which are invariant under non-compact symmetry groups for which the coadjoint orbit space is not Hausdorff. We also show that a G-stable relative equilibrium satisfies the stronger condition of being A-stable, where A is a specific group-theoretically defined subset of G which contains the momentum isotropy subgroup of the relative equilibrium. The results are illustrated by an application to the stability of a rigid body in an ideal irrotational fluid.

Applications of MMPBSA to Membrane Proteins I: Efficient Numerical Solutions of Periodic Poisson-Boltzmann Equation

PubMed Central

Botello-Smith, Wesley M.; Luo, Ray

2016-01-01

Continuum solvent models have been widely used in biomolecular modeling applications. Recently much attention has been given to inclusion of implicit membrane into existing continuum Poisson-Boltzmann solvent models to extend their applications to membrane systems. Inclusion of an implicit membrane complicates numerical solutions of the underlining Poisson-Boltzmann equation due to the dielectric inhomogeneity on the boundary surfaces of a computation grid. This can be alleviated by the use of the periodic boundary condition, a common practice in electrostatic computations in particle simulations. The conjugate gradient and successive over-relaxation methods are relatively straightforward to be adapted to periodic calculations, but their convergence rates are quite low, limiting their applications to free energy simulations that require a large number of conformations to be processed. To accelerate convergence, the Incomplete Cholesky preconditioning and the geometric multi-grid methods have been extended to incorporate periodicity for biomolecular applications. Impressive convergence behaviors were found as in the previous applications of these numerical methods to tested biomolecules and MMPBSA calculations. PMID:26389966

Boundary conditions for the solution of the three-dimensional Poisson equation in open metallic enclosures

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

Biswas, Debabrata; Singh, Gaurav; Kumar, Raghwendra

2015-09-15

Numerical solution of the Poisson equation in metallic enclosures, open at one or more ends, is important in many practical situations, such as high power microwave or photo-cathode devices. It requires imposition of a suitable boundary condition at the open end. In this paper, methods for solving the Poisson equation are investigated for various charge densities and aspect ratios of the open ends. It is found that a mixture of second order and third order local asymptotic boundary conditions is best suited for large aspect ratios, while a proposed non-local matching method, based on the solution of the Laplace equation,more » scores well when the aspect ratio is near unity for all charge density variations, including ones where the centre of charge is close to an open end or the charge density is non-localized. The two methods complement each other and can be used in electrostatic calculations where the computational domain needs to be terminated at the open boundaries of the metallic enclosure.« less

Tensile properties of helical auxetic structures: A numerical study

NASA Astrophysics Data System (ADS)

Wright, J. R.; Sloan, M. R.; Evans, K. E.

2010-08-01

This paper discusses a helical auxetic structure which has a diverse range of practical applications. The mechanical properties of the system can be determined by particular combinations of geometry and component material properties; finite element analysis is used to investigate the static behavior of these structures under tension. Modeling criteria are determined and design issues are discussed. A description of the different strain-dependent mechanical phases is provided. It is shown that the stiffnesses of the component fibers and the initial helical wrap angle are critical design parameters, and that strain-dependent changes in cross-section must be taken into consideration: we observe that the structures exhibit nonlinear behavior due to nonzero component Poisson's ratios. Negative Poisson's ratios for the helical structures as low as -5 are shown. While we focus here on the structure as a yarn our findings are, in principle, scaleable.

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

PubMed

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

2013-09-15

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

Beta-Poisson model for single-cell RNA-seq data analyses.

PubMed

Vu, Trung Nghia; Wills, Quin F; Kalari, Krishna R; Niu, Nifang; Wang, Liewei; Rantalainen, Mattias; Pawitan, Yudi

2016-07-15

Single-cell RNA-sequencing technology allows detection of gene expression at the single-cell level. One typical feature of the data is a bimodality in the cellular distribution even for highly expressed genes, primarily caused by a proportion of non-expressing cells. The standard and the over-dispersed gamma-Poisson models that are commonly used in bulk-cell RNA-sequencing are not able to capture this property. We introduce a beta-Poisson mixture model that can capture the bimodality of the single-cell gene expression distribution. We further integrate the model into the generalized linear model framework in order to perform differential expression analyses. The whole analytical procedure is called BPSC. The results from several real single-cell RNA-seq datasets indicate that ∼90% of the transcripts are well characterized by the beta-Poisson model; the model-fit from BPSC is better than the fit of the standard gamma-Poisson model in > 80% of the transcripts. Moreover, in differential expression analyses of simulated and real datasets, BPSC performs well against edgeR, a conventional method widely used in bulk-cell RNA-sequencing data, and against scde and MAST, two recent methods specifically designed for single-cell RNA-seq data. An R package BPSC for model fitting and differential expression analyses of single-cell RNA-seq data is available under GPL-3 license at https://github.com/nghiavtr/BPSC CONTACT: yudi.pawitan@ki.se or mattias.rantalainen@ki.se Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Angiogenic Signaling in Living Breast Tumor Models

DTIC Science & Technology

2007-06-01

Poisson distributed random noise is added in an amount relative to the desired signal to noise ratio. We fit the data using a regressive fitting...AD_________________ Award Number: W81XWH-05-1-0396 TITLE: Angiogenic Signaling in Living Breast...CONTRACT NUMBER Angiogenic Signaling in Living Breast Tumor Models 5b. GRANT NUMBER W81XWH-05-1-0396 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) 5d

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.

NASCAP user's manual

NASA Technical Reports Server (NTRS)

Mandell, M. J.; Harvey, J. M.; Katz, I.

1977-01-01

The NASCAP (NASA Charging Analyzer Program) code simulates the charging process for a complex object in either tenuous plasma or ground test environment. Detailed specifications needed to run the code are presented. The object definition section, OBJDEF, allows the test object to be easily defined in the cubic mesh. The test object is composed of conducting sections which may be wholly or partially covered with thin dielectric coatings. The potential section, POTENT, obtains the electrostatic potential in the space surrounding the object. It uses the conjugate gradient method to solve the finite element formulation of Poisson's equation. The CHARGE section of NASCAP treats charge redistribution among the surface cells of the object as well as charging through radiation bombardment. NASCAP has facilities for extensive graphical output, including several types of object display plots, potential contour plots, space charge density contour plots, current density plots, and particle trajectory plots.

Repeated Red-Black ordering

NASA Astrophysics Data System (ADS)

Ciarlet, P.

1994-09-01

Hereafter, we describe and analyze, from both a theoretical and a numerical point of view, an iterative method for efficiently solving symmetric elliptic problems with possibly discontinuous coefficients. In the following, we use the Preconditioned Conjugate Gradient method to solve the symmetric positive definite linear systems which arise from the finite element discretization of the problems. We focus our interest on sparse and efficient preconditioners. In order to define the preconditioners, we perform two steps: first we reorder the unknowns and then we carry out a (modified) incomplete factorization of the original matrix. We study numerically and theoretically two preconditioners, the second preconditioner corresponding to the one investigated by Brand and Heinemann [2]. We prove convergence results about the Poisson equation with either Dirichlet or periodic boundary conditions. For a meshsizeh, Brand proved that the condition number of the preconditioned system is bounded byO(h-1/2) for Dirichlet boundary conditions. By slightly modifying the preconditioning process, we prove that the condition number is bounded byO(h-1/3).

Structure-Based Prediction of Unstable Regions in Proteins: Applications to Protein Misfolding Diseases

NASA Astrophysics Data System (ADS)

Guest, Will; Cashman, Neil; Plotkin, Steven

2009-03-01

Protein misfolding is a necessary step in the pathogenesis of many diseases, including Creutzfeldt-Jakob disease (CJD) and familial amyotrophic lateral sclerosis (fALS). Identifying unstable structural elements in their causative proteins elucidates the early events of misfolding and presents targets for inhibition of the disease process. An algorithm was developed to calculate the Gibbs free energy of unfolding for all sequence-contiguous regions of a protein using three methods to parameterize energy changes: a modified G=o model, changes in solvent-accessible surface area, and solution of the Poisson-Boltzmann equation. The entropic effects of disulfide bonds and post-translational modifications are treated analytically. It incorporates a novel method for finding local dielectric constants inside a protein to accurately handle charge effects. We have predicted the unstable parts of prion protein and superoxide dismutase 1, the proteins involved in CJD and fALS respectively, and have used these regions as epitopes to prepare antibodies that are specific to the misfolded conformation and show promise as therapeutic agents.

A Poisson nonnegative matrix factorization method with parameter subspace clustering constraint for endmember extraction in hyperspectral imagery

NASA Astrophysics Data System (ADS)

Sun, Weiwei; Ma, Jun; Yang, Gang; Du, Bo; Zhang, Liangpei

2017-06-01

A new Bayesian method named Poisson Nonnegative Matrix Factorization with Parameter Subspace Clustering Constraint (PNMF-PSCC) has been presented to extract endmembers from Hyperspectral Imagery (HSI). First, the method integrates the liner spectral mixture model with the Bayesian framework and it formulates endmember extraction into a Bayesian inference problem. Second, the Parameter Subspace Clustering Constraint (PSCC) is incorporated into the statistical program to consider the clustering of all pixels in the parameter subspace. The PSCC could enlarge differences among ground objects and helps finding endmembers with smaller spectrum divergences. Meanwhile, the PNMF-PSCC method utilizes the Poisson distribution as the prior knowledge of spectral signals to better explain the quantum nature of light in imaging spectrometer. Third, the optimization problem of PNMF-PSCC is formulated into maximizing the joint density via the Maximum A Posterior (MAP) estimator. The program is finally solved by iteratively optimizing two sub-problems via the Alternating Direction Method of Multipliers (ADMM) framework and the FURTHESTSUM initialization scheme. Five state-of-the art methods are implemented to make comparisons with the performance of PNMF-PSCC on both the synthetic and real HSI datasets. Experimental results show that the PNMF-PSCC outperforms all the five methods in Spectral Angle Distance (SAD) and Root-Mean-Square-Error (RMSE), and especially it could identify good endmembers for ground objects with smaller spectrum divergences.

Development of a fractional-step method for the unsteady incompressible Navier-Stokes equations in generalized coordinate systems

NASA Technical Reports Server (NTRS)

Rosenfeld, Moshe; Kwak, Dochan; Vinokur, Marcel

1992-01-01

A fractional step method is developed for solving the time-dependent three-dimensional incompressible Navier-Stokes equations in generalized coordinate systems. The primitive variable formulation uses the pressure, defined at the center of the computational cell, and the volume fluxes across the faces of the cells as the dependent variables, instead of the Cartesian components of the velocity. This choice is equivalent to using the contravariant velocity components in a staggered grid multiplied by the volume of the computational cell. The governing equations are discretized by finite volumes using a staggered mesh system. The solution of the continuity equation is decoupled from the momentum equations by a fractional step method which enforces mass conservation by solving a Poisson equation. This procedure, combined with the consistent approximations of the geometric quantities, is done to satisfy the discretized mass conservation equation to machine accuracy, as well as to gain the favorable convergence properties of the Poisson solver. The momentum equations are solved by an approximate factorization method, and a novel ZEBRA scheme with four-color ordering is devised for the efficient solution of the Poisson equation. Several two- and three-dimensional laminar test cases are computed and compared with other numerical and experimental results to validate the solution method. Good agreement is obtained in all cases.

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.

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.

A network thermodynamic method for numerical solution of the Nernst-Planck and Poisson equation system with application to ionic transport through membranes.

PubMed

Horno, J; González-Caballero, F; González-Fernández, C F

1990-01-01

Simple techniques of network thermodynamics are used to obtain the numerical solution of the Nernst-Planck and Poisson equation system. A network model for a particular physical situation, namely ionic transport through a thin membrane with simultaneous diffusion, convection and electric current, is proposed. Concentration and electric field profiles across the membrane, as well as diffusion potential, have been simulated using the electric circuit simulation program, SPICE. The method is quite general and extremely efficient, permitting treatments of multi-ion systems whatever the boundary and experimental conditions may be.

Evaluation of lattice sums by the Poisson sum formula

NASA Technical Reports Server (NTRS)

Ray, R. D.

1975-01-01

The Poisson sum formula was applied to the problem of summing pairwise interactions between an observer molecule and a semi-infinite regular array of solid state molecules. The transformed sum is often much more rapidly convergent than the original sum, and forms a Fourier series in the solid surface coordinates. The method is applicable to a variety of solid state structures and functional forms of the pairwise potential. As an illustration of the method, the electric field above the (100) face of the CsCl structure is calculated and compared to earlier results obtained by direct summation.

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

PubMed Central

Nguyen, Thien; Karčiauskas, Kęstutis; Peters, Jörg

2015-01-01

Geometrically continuous (Gk) constructions naturally yield families of finite elements for isogeometric analysis (IGA) that are Ck also for non-tensor-product layout. This paper describes and analyzes one such concrete C1 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 G1 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(h3) 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. PMID:26594070

Solution of Poisson equations for 3-dimensional grid generations. [computations of a flow field over a thin delta wing

NASA Technical Reports Server (NTRS)

Fujii, K.

1983-01-01

A method for generating three dimensional, finite difference grids about complicated geometries by using Poisson equations is developed. The inhomogenous terms are automatically chosen such that orthogonality and spacing restrictions at the body surface are satisfied. Spherical variables are used to avoid the axis singularity, and an alternating-direction-implicit (ADI) solution scheme is used to accelerate the computations. Computed results are presented that show the capability of the method. Since most of the results presented have been used as grids for flow-field computations, this is indicative that the method is a useful tool for generating three-dimensional grids about complicated geometries.

Mixed effect Poisson log-linear models for clinical and epidemiological sleep hypnogram data

PubMed Central

Swihart, Bruce J.; Caffo, Brian S.; Crainiceanu, Ciprian; Punjabi, Naresh M.

2013-01-01

Bayesian Poisson log-linear multilevel models scalable to epidemiological studies are proposed to investigate population variability in sleep state transition rates. Hierarchical random effects are used to account for pairings of subjects and repeated measures within those subjects, as comparing diseased to non-diseased subjects while minimizing bias is of importance. Essentially, non-parametric piecewise constant hazards are estimated and smoothed, allowing for time-varying covariates and segment of the night comparisons. The Bayesian Poisson regression is justified through a re-derivation of a classical algebraic likelihood equivalence of Poisson regression with a log(time) offset and survival regression assuming exponentially distributed survival times. Such re-derivation allows synthesis of two methods currently used to analyze sleep transition phenomena: stratified multi-state proportional hazards models and log-linear models with GEE for transition counts. An example data set from the Sleep Heart Health Study is analyzed. Supplementary material includes the analyzed data set as well as the code for a reproducible analysis. PMID:22241689

Combinatorial Formulas for Characteristic Classes, and Localization of Secondary Topological Invariants.

NASA Astrophysics Data System (ADS)

Smirnov, Mikhail

1995-01-01

The problems solved in this thesis originated from combinatorial formulas for characteristic classes. This thesis deals with Chern-Simons classes, their generalizations and related algebraic and analytic problems. (1) In this thesis, I describe a new class of algebras whose elements contain Chern and generalized Chern -Simons classes. There is a Poisson bracket in these algebras, similar to the bracket in Kontsevich's noncommutative symplectic geometry (Kon). I prove that the Poisson bracket gives rise to a graded Lie algebra containing differential forms representing Chern and Chern-Simons classes. This is a new result. I describe algebraic analogs of the dilogarithm and higher polylogarithms in the algebra corresponding to Chern-Simons classes. (2) I study the properties of this bracket. It is possible to write the exterior differential and other operations in the algebra using this bracket. The bracket of any two Chern classes is zero and the bracket of a Chern class and a Chern-Simons class is d-closed. The construction developed here easily gives explicit formulas for known secondary classes and makes it possible to construct new ones. (3) I develop an algebraic model for the action of the gauge group and describe how elements of algebra corresponding to the secondary characteristic classes change under this action (see theorem 3 page xi). (4) It is possible give new explicit formulas for cocycles on a gauge group of a bundle and for the corresponding cocycles on the Lie algebra of the gauge group. I use formulas for secondary characteristic classes and an algebraic approach developed in chapter 1. I also use the work of Faddeev, Reiman and Semyonov-Tian-Shanskii (FRS) on cocycles as quantum anomalies. (5) I apply the methods of differential geometry of formal power series to construct universal characteristic and secondary characteristic classes. Given a pair of gauge equivalent connections using local formulas I obtain dilogarithmic and trilogarithmic analogs of Chern-Simons classes.

Acceleration of incremental-pressure-correction incompressible flow computations using a coarse-grid projection method

NASA Astrophysics Data System (ADS)

Kashefi, Ali; Staples, Anne

2016-11-01

Coarse grid projection (CGP) methodology is a novel multigrid method for systems involving decoupled nonlinear evolution equations and linear elliptic equations. The nonlinear equations are solved on a fine grid and the linear equations are solved on a corresponding coarsened grid. Mapping functions transfer data between the two grids. Here we propose a version of CGP for incompressible flow computations using incremental pressure correction methods, called IFEi-CGP (implicit-time-integration, finite-element, incremental coarse grid projection). Incremental pressure correction schemes solve Poisson's equation for an intermediate variable and not the pressure itself. This fact contributes to IFEi-CGP's efficiency in two ways. First, IFEi-CGP preserves the velocity field accuracy even for a high level of pressure field grid coarsening and thus significant speedup is achieved. Second, because incremental schemes reduce the errors that arise from boundaries with artificial homogenous Neumann conditions, CGP generates undamped flows for simulations with velocity Dirichlet boundary conditions. Comparisons of the data accuracy and CPU times for the incremental-CGP versus non-incremental-CGP computations are presented.

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.

A comparison of multiple indicator kriging and area-to-point Poisson kriging for mapping patterns of herbivore species abundance in Kruger National Park, South Africa

PubMed Central

Kerry, Ruth; Goovaerts, Pierre; Smit, Izak P.J.; Ingram, Ben R.

2015-01-01

Kruger National Park (KNP), South Africa, provides protected habitats for the unique animals of the African savannah. For the past 40 years, annual aerial surveys of herbivores have been conducted to aid management decisions based on (1) the spatial distribution of species throughout the park and (2) total species populations in a year. The surveys are extremely time consuming and costly. For many years, the whole park was surveyed, but in 1998 a transect survey approach was adopted. This is cheaper and less time consuming but leaves gaps in the data spatially. Also the distance method currently employed by the park only gives estimates of total species populations but not their spatial distribution. We compare the ability of multiple indicator kriging and area-to-point Poisson kriging to accurately map species distribution in the park. A leave-one-out cross-validation approach indicates that multiple indicator kriging makes poor estimates of the number of animals, particularly the few large counts, as the indicator variograms for such high thresholds are pure nugget. Poisson kriging was applied to the prediction of two types of abundance data: spatial density and proportion of a given species. Both Poisson approaches had standardized mean absolute errors (St. MAEs) of animal counts at least an order of magnitude lower than multiple indicator kriging. The spatial density, Poisson approach (1), gave the lowest St. MAEs for the most abundant species and the proportion, Poisson approach (2), did for the least abundant species. Incorporating environmental data into Poisson approach (2) further reduced St. MAEs. PMID:25729318

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.

A comparison of multiple indicator kriging and area-to-point Poisson kriging for mapping patterns of herbivore species abundance in Kruger National Park, South Africa.

PubMed

Kerry, Ruth; Goovaerts, Pierre; Smit, Izak P J; Ingram, Ben R

Kruger National Park (KNP), South Africa, provides protected habitats for the unique animals of the African savannah. For the past 40 years, annual aerial surveys of herbivores have been conducted to aid management decisions based on (1) the spatial distribution of species throughout the park and (2) total species populations in a year. The surveys are extremely time consuming and costly. For many years, the whole park was surveyed, but in 1998 a transect survey approach was adopted. This is cheaper and less time consuming but leaves gaps in the data spatially. Also the distance method currently employed by the park only gives estimates of total species populations but not their spatial distribution. We compare the ability of multiple indicator kriging and area-to-point Poisson kriging to accurately map species distribution in the park. A leave-one-out cross-validation approach indicates that multiple indicator kriging makes poor estimates of the number of animals, particularly the few large counts, as the indicator variograms for such high thresholds are pure nugget. Poisson kriging was applied to the prediction of two types of abundance data: spatial density and proportion of a given species. Both Poisson approaches had standardized mean absolute errors (St. MAEs) of animal counts at least an order of magnitude lower than multiple indicator kriging. The spatial density, Poisson approach (1), gave the lowest St. MAEs for the most abundant species and the proportion, Poisson approach (2), did for the least abundant species. Incorporating environmental data into Poisson approach (2) further reduced St. MAEs.

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.

Fourier ptychographic reconstruction using Poisson maximum likelihood and truncated Wirtinger gradient.

PubMed

Bian, Liheng; Suo, Jinli; Chung, Jaebum; Ou, Xiaoze; Yang, Changhuei; Chen, Feng; Dai, Qionghai

2016-06-10

Fourier ptychographic microscopy (FPM) is a novel computational coherent imaging technique for high space-bandwidth product imaging. Mathematically, Fourier ptychographic (FP) reconstruction can be implemented as a phase retrieval optimization process, in which we only obtain low resolution intensity images corresponding to the sub-bands of the sample's high resolution (HR) spatial spectrum, and aim to retrieve the complex HR spectrum. In real setups, the measurements always suffer from various degenerations such as Gaussian noise, Poisson noise, speckle noise and pupil location error, which would largely degrade the reconstruction. To efficiently address these degenerations, we propose a novel FP reconstruction method under a gradient descent optimization framework in this paper. The technique utilizes Poisson maximum likelihood for better signal modeling, and truncated Wirtinger gradient for effective error removal. Results on both simulated data and real data captured using our laser-illuminated FPM setup show that the proposed method outperforms other state-of-the-art algorithms. Also, we have released our source code for non-commercial use.

Poissonian renormalizations, exponentials, and power laws.

PubMed

Eliazar, Iddo

2013-05-01

This paper presents a comprehensive "renormalization study" of Poisson processes governed by exponential and power-law intensities. These Poisson processes are of fundamental importance, as they constitute the very bedrock of the universal extreme-value laws of Gumbel, Fréchet, and Weibull. Applying the method of Poissonian renormalization we analyze the emergence of these Poisson processes, unveil their intrinsic dynamical structures, determine their domains of attraction, and characterize their structural phase transitions. These structural phase transitions are shown to be governed by uniform and harmonic intensities, to have universal domains of attraction, to uniquely display intrinsic invariance, and to be intimately connected to "white noise" and to "1/f noise." Thus, we establish a Poissonian explanation to the omnipresence of white and 1/f noises.

Poisson sigma models, reduction and nonlinear gauge theories

NASA Astrophysics Data System (ADS)

Signori, Daniele

This dissertation comprises two main lines of research. Firstly, we study non-linear gauge theories for principal bundles, where the structure group is replaced by a Lie groupoid. We follow the approach of Moerdijk-Mrcun and establish its relation with the existing physics literature. In particular, we derive a new formula for the gauge transformation which closely resembles and generalizes the classical formulas found in Yang Mills gauge theories. Secondly, we give a field theoretic interpretation of the of the BRST (Becchi-Rouet-Stora-Tyutin) and BFV (Batalin-Fradkin-Vilkovisky) methods for the reduction of coisotropic submanifolds of Poisson manifolds. The generalized Poisson sigma models that we define are related to the quantization deformation problems of coisotropic submanifolds using homotopical algebras.

Nonparametric estimation of the heterogeneity of a random medium using compound Poisson process modeling of wave multiple scattering.

PubMed

Le Bihan, Nicolas; Margerin, Ludovic

2009-07-01

In this paper, we present a nonparametric method to estimate the heterogeneity of a random medium from the angular distribution of intensity of waves transmitted through a slab of random material. Our approach is based on the modeling of forward multiple scattering using compound Poisson processes on compact Lie groups. The estimation technique is validated through numerical simulations based on radiative transfer theory.

A note on an attempt at more efficient Poisson series evaluation. [for lunar libration

NASA Technical Reports Server (NTRS)

Shelus, P. J.; Jefferys, W. H., III

1975-01-01

A substantial reduction has been achieved in the time necessary to compute lunar libration series. The method involves eliminating many of the trigonometric function calls by a suitable transformation and applying a short SNOBOL processor to the FORTRAN coding of the transformed series, which obviates many of the multiplication operations during the course of series evaluation. It is possible to accomplish similar results quite easily with other Poisson series.

Integración automatizada de las ecuaciones de Lagrange en el movimiento orbital.

NASA Astrophysics Data System (ADS)

Abad, A.; San Juan, J. F.

The new techniques of algebraic manipulation, especially the Poisson Series Processor, permit the analytical integration of the more and more complex problems of celestial mechanics. The authors are developing a new Poisson Series Processor, PSPC, and they use it to solve the Lagrange equation of the orbital motion. They integrate the Lagrange equation by using the stroboscopic method, and apply it to the main problem of the artificial satellite theory.

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.

Exploring spatial patterns of sudden cardiac arrests in the city of Toronto using Poisson kriging and Hot Spot analyses

PubMed Central

2017-01-01

Introduction Our study looked at out-of-hospital sudden cardiac arrest events in the City of Toronto. These are relatively rare events, yet present a serious global clinical and public health problem. We report on the application of spatial methods and tools that, although relatively well known to geographers and natural resource scientists, need to become better known and used more frequently by health care researchers. Materials and methods Our data came from the population-based Rescu Epistry cardiac arrest database. We limited it to the residents of the City of Toronto who experienced sudden arrest in 2010. The data was aggregated at the Dissemination Area level, and population rates were calculated. Poisson kriging was carried out on one year of data using three different spatial weights. Kriging estimates were then compared in Hot Spot analyses. Results Spatial analysis revealed that Poisson kriging can yield reliable rates using limited data of high quality. We observed the highest rates of sudden arrests in the north and central parts of Etobicoke, western parts of North York as well as the central and southwestern parts of Scarborough while the lowest rates were found in north and eastern parts of Scarborough, downtown Toronto, and East York as well as east central parts of North York. Influence of spatial neighbours on the results did not extend past two rings of adjacent units. Conclusions Poisson kriging has the potential to be applied to a wide range of healthcare research, particularly on rare events. This approach can be successfully combined with other spatial methods. More applied research, is needed to establish a wider acceptance for this method, especially among healthcare researchers and epidemiologists. PMID:28672029

Discrimination between native and intentionally misfolded conformations of proteins: ES/IS, a new method for calculating conformational free energy that uses both dynamics simulations with an explicit solvent and an implicit solvent continuum model.

PubMed

Vorobjev, Y N; Almagro, J C; Hermans, J

1998-09-01

A new method for calculating the total conformational free energy of proteins in water solvent is presented. The method consists of a relatively brief simulation by molecular dynamics with explicit solvent (ES) molecules to produce a set of microstates of the macroscopic conformation. Conformational energy and entropy are obtained from the simulation, the latter in the quasi-harmonic approximation by analysis of the covariance matrix. The implicit solvent (IS) dielectric continuum model is used to calculate the average solvation free energy as the sum of the free energies of creating the solute-size hydrophobic cavity, of the van der Waals solute-solvent interactions, and of the polarization of water solvent by the solute's charges. The reliability of the solvation free energy depends on a number of factors: the details of arrangement of the protein's charges, especially those near the surface; the definition of the molecular surface; and the method chosen for solving the Poisson equation. Molecular dynamics simulation in explicit solvent relaxes the protein's conformation and allows polar surface groups to assume conformations compatible with interaction with solvent, while averaging of internal energy and solvation free energy tend to enhance the precision. Two recently developed methods--SIMS, for calculation of a smooth invariant molecular surface, and FAMBE, for solution of the Poisson equation via a fast adaptive multigrid boundary element--have been employed. The SIMS and FAMBE programs scale linearly with the number of atoms. SIMS is superior to Connolly's MS (molecular surface) program: it is faster, more accurate, and more stable, and it smooths singularities of the molecular surface. Solvation free energies calculated with these two programs do not depend on molecular position or orientation and are stable along a molecular dynamics trajectory. We have applied this method to calculate the conformational free energy of native and intentionally misfolded globular conformations of proteins (the EMBL set of deliberately misfolded proteins) and have obtained good discrimination in favor of the native conformations in all instances.

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

DTIC Science & Technology

1987-10-10

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

A flexible count data model to fit the wide diversity of expression profiles arising from extensively replicated RNA-seq experiments

PubMed Central

2013-01-01

Background High-throughput RNA sequencing (RNA-seq) offers unprecedented power to capture the real dynamics of gene expression. Experimental designs with extensive biological replication present a unique opportunity to exploit this feature and distinguish expression profiles with higher resolution. RNA-seq data analysis methods so far have been mostly applied to data sets with few replicates and their default settings try to provide the best performance under this constraint. These methods are based on two well-known count data distributions: the Poisson and the negative binomial. The way to properly calibrate them with large RNA-seq data sets is not trivial for the non-expert bioinformatics user. Results Here we show that expression profiles produced by extensively-replicated RNA-seq experiments lead to a rich diversity of count data distributions beyond the Poisson and the negative binomial, such as Poisson-Inverse Gaussian or Pólya-Aeppli, which can be captured by a more general family of count data distributions called the Poisson-Tweedie. The flexibility of the Poisson-Tweedie family enables a direct fitting of emerging features of large expression profiles, such as heavy-tails or zero-inflation, without the need to alter a single configuration parameter. We provide a software package for R called tweeDEseq implementing a new test for differential expression based on the Poisson-Tweedie family. Using simulations on synthetic and real RNA-seq data we show that tweeDEseq yields P-values that are equally or more accurate than competing methods under different configuration parameters. By surveying the tiny fraction of sex-specific gene expression changes in human lymphoblastoid cell lines, we also show that tweeDEseq accurately detects differentially expressed genes in a real large RNA-seq data set with improved performance and reproducibility over the previously compared methodologies. Finally, we compared the results with those obtained from microarrays in order to check for reproducibility. Conclusions RNA-seq data with many replicates leads to a handful of count data distributions which can be accurately estimated with the statistical model illustrated in this paper. This method provides a better fit to the underlying biological variability; this may be critical when comparing groups of RNA-seq samples with markedly different count data distributions. The tweeDEseq package forms part of the Bioconductor project and it is available for download at http://www.bioconductor.org. PMID:23965047

On the velocity space discretization for the Vlasov-Poisson system: Comparison between implicit Hermite spectral and Particle-in-Cell methods

NASA Astrophysics Data System (ADS)

Camporeale, E.; Delzanno, G. L.; Bergen, B. K.; Moulton, J. D.

2016-01-01

We describe a spectral method for the numerical solution of the Vlasov-Poisson system where the velocity space is decomposed by means of an Hermite basis, and the configuration space is discretized via a Fourier decomposition. The novelty of our approach is an implicit time discretization that allows exact conservation of charge, momentum and energy. The computational efficiency and the cost-effectiveness of this method are compared to the fully-implicit PIC method recently introduced by Markidis and Lapenta (2011) and Chen et al. (2011). The following examples are discussed: Langmuir wave, Landau damping, ion-acoustic wave, two-stream instability. The Fourier-Hermite spectral method can achieve solutions that are several orders of magnitude more accurate at a fraction of the cost with respect to PIC.

Generic Schemes for Single-Molecule Kinetics. 2: Information Content of the Poisson Indicator.

PubMed

Avila, Thomas R; Piephoff, D Evan; Cao, Jianshu

2017-08-24

Recently, we described a pathway analysis technique (paper 1) for analyzing generic schemes for single-molecule kinetics based upon the first-passage time distribution. Here, we employ this method to derive expressions for the Poisson indicator, a normalized measure of stochastic variation (essentially equivalent to the Fano factor and Mandel's Q parameter), for various renewal (i.e., memoryless) enzymatic reactions. We examine its dependence on substrate concentration, without assuming all steps follow Poissonian kinetics. Based upon fitting to the functional forms of the first two waiting time moments, we show that, to second order, the non-Poissonian kinetics are generally underdetermined but can be specified in certain scenarios. For an enzymatic reaction with an arbitrary intermediate topology, we identify a generic minimum of the Poisson indicator as a function of substrate concentration, which can be used to tune substrate concentration to the stochastic fluctuations and to estimate the largest number of underlying consecutive links in a turnover cycle. We identify a local maximum of the Poisson indicator (with respect to substrate concentration) for a renewal process as a signature of competitive binding, either between a substrate and an inhibitor or between multiple substrates. Our analysis explores the rich connections between Poisson indicator measurements and microscopic kinetic mechanisms.

Stiffness of frictional contact of dissimilar elastic solids

DOE PAGES

Lee, Jin Haeng; Gao, Yanfei; Bower, Allan F.; ...

2017-12-22

The classic Sneddon relationship between the normal contact stiffness and the contact size is valid for axisymmetric, frictionless contact, in which the two contacting solids are approximated by elastic half-spaces. Deviation from this result critically affects the accuracy of the load and displacement sensing nanoindentation techniques. This study gives a thorough numerical and analytical investigation of corrections needed to the Sneddon solution when finite Coulomb friction exists between an elastic half-space and a flat-ended rigid punch with circular or noncircular shape. Because of linearity of the Coulomb friction, the correction factor is found to be a function of the frictionmore » coefficient, Poisson's ratio, and the contact shape, but independent of the contact size. Two issues are of primary concern in the finite element simulations – adequacy of the mesh near the contact edge and the friction implementation methodology. Although the stick or slip zone sizes are quite different from the penalty or Lagrangian methods, the calculated contact stiffnesses are almost the same and may be considerably larger than those in Sneddon's solution. For circular punch contact, the numerical solutions agree remarkably well with a previous analytical solution. For non-circular punch contact, the results can be represented using the equivalence between the contact problem and bi-material fracture mechanics. Finally, the correction factor is found to be a product of that for the circular contact and a multiplicative factor that depends only on the shape of the punch but not on the friction coefficient or Poisson's ratio.« less

Stiffness of frictional contact of dissimilar elastic solids

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

Lee, Jin Haeng; Gao, Yanfei; Bower, Allan F.

The classic Sneddon relationship between the normal contact stiffness and the contact size is valid for axisymmetric, frictionless contact, in which the two contacting solids are approximated by elastic half-spaces. Deviation from this result critically affects the accuracy of the load and displacement sensing nanoindentation techniques. This study gives a thorough numerical and analytical investigation of corrections needed to the Sneddon solution when finite Coulomb friction exists between an elastic half-space and a flat-ended rigid punch with circular or noncircular shape. Because of linearity of the Coulomb friction, the correction factor is found to be a function of the frictionmore » coefficient, Poisson's ratio, and the contact shape, but independent of the contact size. Two issues are of primary concern in the finite element simulations – adequacy of the mesh near the contact edge and the friction implementation methodology. Although the stick or slip zone sizes are quite different from the penalty or Lagrangian methods, the calculated contact stiffnesses are almost the same and may be considerably larger than those in Sneddon's solution. For circular punch contact, the numerical solutions agree remarkably well with a previous analytical solution. For non-circular punch contact, the results can be represented using the equivalence between the contact problem and bi-material fracture mechanics. Finally, the correction factor is found to be a product of that for the circular contact and a multiplicative factor that depends only on the shape of the punch but not on the friction coefficient or Poisson's ratio.« less

Stiffness of frictional contact of dissimilar elastic solids

NASA Astrophysics Data System (ADS)

Lee, Jin Haeng; Gao, Yanfei; Bower, Allan F.; Xu, Haitao; Pharr, George M.

2018-03-01

The classic Sneddon relationship between the normal contact stiffness and the contact size is valid for axisymmetric, frictionless contact, in which the two contacting solids are approximated by elastic half-spaces. Deviation from this result critically affects the accuracy of the load and displacement sensing nanoindentation techniques. This paper gives a thorough numerical and analytical investigation of corrections needed to the Sneddon solution when finite Coulomb friction exists between an elastic half-space and a flat-ended rigid punch with circular or noncircular shape. Because of linearity of the Coulomb friction, the correction factor is found to be a function of the friction coefficient, Poisson's ratio, and the contact shape, but independent of the contact size. Two issues are of primary concern in the finite element simulations - adequacy of the mesh near the contact edge and the friction implementation methodology. Although the stick or slip zone sizes are quite different from the penalty or Lagrangian methods, the calculated contact stiffnesses are almost the same and may be considerably larger than those in Sneddon's solution. For circular punch contact, the numerical solutions agree remarkably well with a previous analytical solution. For non-circular punch contact, the results can be represented using the equivalence between the contact problem and bi-material fracture mechanics. The correction factor is found to be a product of that for the circular contact and a multiplicative factor that depends only on the shape of the punch but not on the friction coefficient or Poisson's ratio.

Functional Data Approximation on Bounded Domains using Polygonal Finite Elements.

PubMed

Cao, Juan; Xiao, Yanyang; Chen, Zhonggui; Wang, Wenping; Bajaj, Chandrajit

2018-07-01

We construct and analyze piecewise approximations of functional data on arbitrary 2D bounded domains using generalized barycentric finite elements, and particularly quadratic serendipity elements for planar polygons. We compare approximation qualities (precision/convergence) of these partition-of-unity finite elements through numerical experiments, using Wachspress coordinates, natural neighbor coordinates, Poisson coordinates, mean value coordinates, and quadratic serendipity bases over polygonal meshes on the domain. For a convex n -sided polygon, the quadratic serendipity elements have 2 n basis functions, associated in a Lagrange-like fashion to each vertex and each edge midpoint, rather than the usual n ( n + 1)/2 basis functions to achieve quadratic convergence. Two greedy algorithms are proposed to generate Voronoi meshes for adaptive functional/scattered data approximations. Experimental results show space/accuracy advantages for these quadratic serendipity finite elements on polygonal domains versus traditional finite elements over simplicial meshes. Polygonal meshes and parameter coefficients of the quadratic serendipity finite elements obtained by our greedy algorithms can be further refined using an L 2 -optimization to improve the piecewise functional approximation. We conduct several experiments to demonstrate the efficacy of our algorithm for modeling features/discontinuities in functional data/image approximation.

Monitoring Poisson's Ratio Degradation of FRP Composites under Fatigue Loading Using Biaxially Embedded FBG Sensors.

PubMed

Akay, Erdem; Yilmaz, Cagatay; Kocaman, Esat S; Turkmen, Halit S; Yildiz, Mehmet

2016-09-19

The significance of strain measurement is obvious for the analysis of Fiber-Reinforced Polymer (FRP) composites. Conventional strain measurement methods are sufficient for static testing in general. Nevertheless, if the requirements exceed the capabilities of these conventional methods, more sophisticated techniques are necessary to obtain strain data. Fiber Bragg Grating (FBG) sensors have many advantages for strain measurement over conventional ones. Thus, the present paper suggests a novel method for biaxial strain measurement using embedded FBG sensors during the fatigue testing of FRP composites. Poisson's ratio and its reduction were monitored for each cyclic loading by using embedded FBG sensors for a given specimen and correlated with the fatigue stages determined based on the variations of the applied fatigue loading and temperature due to the autogenous heating to predict an oncoming failure of the continuous fiber-reinforced epoxy matrix composite specimens under fatigue loading. The results show that FBG sensor technology has a remarkable potential for monitoring the evolution of Poisson's ratio on a cycle-by-cycle basis, which can reliably be used towards tracking the fatigue stages of composite for structural health monitoring purposes.

Multiscale modeling of a rectifying bipolar nanopore: Comparing Poisson-Nernst-Planck to Monte Carlo

NASA Astrophysics Data System (ADS)

Matejczyk, Bartłomiej; Valiskó, Mónika; Wolfram, Marie-Therese; Pietschmann, Jan-Frederik; Boda, Dezső

2017-03-01

In the framework of a multiscale modeling approach, we present a systematic study of a bipolar rectifying nanopore using a continuum and a particle simulation method. The common ground in the two methods is the application of the Nernst-Planck (NP) equation to compute ion transport in the framework of the implicit-water electrolyte model. The difference is that the Poisson-Boltzmann theory is used in the Poisson-Nernst-Planck (PNP) approach, while the Local Equilibrium Monte Carlo (LEMC) method is used in the particle simulation approach (NP+LEMC) to relate the concentration profile to the electrochemical potential profile. Since we consider a bipolar pore which is short and narrow, we perform simulations using two-dimensional PNP. In addition, results of a non-linear version of PNP that takes crowding of ions into account are shown. We observe that the mean field approximation applied in PNP is appropriate to reproduce the basic behavior of the bipolar nanopore (e.g., rectification) for varying parameters of the system (voltage, surface charge, electrolyte concentration, and pore radius). We present current data that characterize the nanopore's behavior as a device, as well as concentration, electrical potential, and electrochemical potential profiles.

Multiscale modeling of a rectifying bipolar nanopore: Comparing Poisson-Nernst-Planck to Monte Carlo.

PubMed

Matejczyk, Bartłomiej; Valiskó, Mónika; Wolfram, Marie-Therese; Pietschmann, Jan-Frederik; Boda, Dezső

2017-03-28

In the framework of a multiscale modeling approach, we present a systematic study of a bipolar rectifying nanopore using a continuum and a particle simulation method. The common ground in the two methods is the application of the Nernst-Planck (NP) equation to compute ion transport in the framework of the implicit-water electrolytemodel. The difference is that the Poisson-Boltzmann theory is used in the Poisson-Nernst-Planck (PNP) approach, while the Local Equilibrium Monte Carlo (LEMC) method is used in the particle simulation approach (NP+LEMC) to relate the concentration profile to the electrochemical potential profile. Since we consider a bipolar pore which is short and narrow, we perform simulations using two-dimensional PNP. In addition, results of a non-linear version of PNP that takes crowding of ions into account are shown. We observe that the mean field approximation applied in PNP is appropriate to reproduce the basic behavior of the bipolar nanopore (e.g., rectification) for varying parameters of the system (voltage, surface charge,electrolyte concentration, and pore radius). We present current data that characterize the nanopore's behavior as a device, as well as concentration, electrical potential, and electrochemical potential profiles.

Multiparameter linear least-squares fitting to Poisson data one count at a time

NASA Technical Reports Server (NTRS)

Wheaton, Wm. A.; Dunklee, Alfred L.; Jacobsen, Allan S.; Ling, James C.; Mahoney, William A.; Radocinski, Robert G.

1995-01-01

A standard problem in gamma-ray astronomy data analysis is the decomposition of a set of observed counts, described by Poisson statistics, according to a given multicomponent linear model, with underlying physical count rates or fluxes which are to be estimated from the data. Despite its conceptual simplicity, the linear least-squares (LLSQ) method for solving this problem has generally been limited to situations in which the number n(sub i) of counts in each bin i is not too small, conventionally more than 5-30. It seems to be widely believed that the failure of the LLSQ method for small counts is due to the failure of the Poisson distribution to be even approximately normal for small numbers. The cause is more accurately the strong anticorrelation between the data and the wieghts w(sub i) in the weighted LLSQ method when square root of n(sub i) instead of square root of bar-n(sub i) is used to approximate the uncertainties, sigma(sub i), in the data, where bar-n(sub i) = E(n(sub i)), the expected value of N(sub i). We show in an appendix that, avoiding this approximation, the correct equations for the Poisson LLSQ (PLLSQ) problems are actually identical to those for the maximum likelihood estimate using the exact Poisson distribution. We apply the method to solve a problem in high-resolution gamma-ray spectroscopy for the JPL High-Resolution Gamma-Ray Spectrometer flown on HEAO 3. Systematic error in subtracting the strong, highly variable background encountered in the low-energy gamma-ray region can be significantly reduced by closely pairing source and background data in short segments. Significant results can be built up by weighted averaging of the net fluxes obtained from the subtraction of many individual source/background pairs. Extension of the approach to complex situations, with multiple cosmic sources and realistic background parameterizations, requires a means of efficiently fitting to data from single scans in the narrow (approximately = 1.2 keV, HEAO 3) energy channels of a Ge spectrometer, where the expected number of counts obtained per scan may be very low. Such an analysis system is discussed and compared to the method previously used.

IETI – Isogeometric Tearing and Interconnecting

PubMed Central

Kleiss, Stefan K.; Pechstein, Clemens; Jüttler, Bert; Tomar, Satyendra

2012-01-01

Finite Element Tearing and Interconnecting (FETI) methods are a powerful approach to designing solvers for large-scale problems in computational mechanics. The numerical simulation problem is subdivided into a number of independent sub-problems, which are then coupled in appropriate ways. NURBS- (Non-Uniform Rational B-spline) based isogeometric analysis (IGA) applied to complex geometries requires to represent the computational domain as a collection of several NURBS geometries. Since there is a natural decomposition of the computational domain into several subdomains, NURBS-based IGA is particularly well suited for using FETI methods. This paper proposes the new IsogEometric Tearing and Interconnecting (IETI) method, which combines the advanced solver design of FETI with the exact geometry representation of IGA. We describe the IETI framework for two classes of simple model problems (Poisson and linearized elasticity) and discuss the coupling of the subdomains along interfaces (both for matching interfaces and for interfaces with T-joints, i.e. hanging nodes). Special attention is paid to the construction of a suitable preconditioner for the iterative linear solver used for the interface problem. We report several computational experiments to demonstrate the performance of the proposed IETI method. PMID:24511167

A novel approach for extracting viscoelastic parameters of living cells through combination of inverse finite element simulation and Atomic Force Microscopy.

PubMed

Wei, Fanan; Yang, Haitao; Liu, Lianqing; Li, Guangyong

2017-03-01

Dynamic mechanical behaviour of living cells has been described by viscoelasticity. However, quantitation of the viscoelastic parameters for living cells is far from sophisticated. In this paper, combining inverse finite element (FE) simulation with Atomic Force Microscope characterization, we attempt to develop a new method to evaluate and acquire trustworthy viscoelastic index of living cells. First, influence of the experiment parameters on stress relaxation process is assessed using FE simulation. As suggested by the simulations, cell height has negligible impact on shape of the force-time curve, i.e. the characteristic relaxation time; and the effect originates from substrate can be totally eliminated when stiff substrate (Young's modulus larger than 3 GPa) is used. Then, so as to develop an effective optimization strategy for the inverse FE simulation, the parameters sensitivity evaluation is performed for Young's modulus, Poisson's ratio, and characteristic relaxation time. With the experiment data obtained through typical stress relaxation measurement, viscoelastic parameters are extracted through the inverse FE simulation by comparing the simulation results and experimental measurements. Finally, reliability of the acquired mechanical parameters is verified with different load experiments performed on the same cell.

Lunar Proton Albedo Anomalies: Soil, Surveyors, and Statistics

NASA Astrophysics Data System (ADS)

Wilson, J. K.; Schwadron, N.; Spence, H. E.; Case, A. W.; Golightly, M. J.; Jordan, A.; Looper, M. D.; Petro, N. E.; Robinson, M. S.; Stubbs, T. J.; Zeitlin, C. J.; Blake, J. B.; Kasper, J. C.; Mazur, J. E.; Smith, S. S.; Townsend, L. W.

2014-12-01

Since the launch of LRO in 2009, the CRaTER instrument has been mapping albedo protons (~100 MeV) from the Moon. These protons are produced by nuclear spallation, a consequence of galactic cosmic ray (GCR) bombardment of the lunar regolith. Just as spalled neutrons and gamma rays reveal elemental abundances in the lunar regolith, albedo protons may be a complimentary method for mapping compositional variations. We presently find that the lunar maria have an average proton yield 0.9% ±0.3% higher than the average yield in the highlands; this is consistent with neutron data that is sensitive to the regolith's average atomic weight. We also see cases where two or more adjacent pixels (15° × 15°) have significantly anomalous yields above or below the mean. These include two high-yielding regions in the maria, and three low-yielding regions in the far-side highlands. Some of the regions could be artifacts of Poisson noise, but for completeness we consider possible effects from compositional anomalies in the lunar regolith, including pyroclastic flows, antipodes of fresh craters, and so-called "red spots". We also consider man-made landers and crash sites that may have brought elements not normally found in the lunar regolith.

In situ MEMS testing: correlation of high-resolution X-ray diffraction with mechanical experiments and finite element analysis.

PubMed

Schifferle, Andreas; Dommann, Alex; Neels, Antonia

2017-01-01

New methods are needed in microsystems technology for evaluating microelectromechanical systems (MEMS) because of their reduced size. The assessment and characterization of mechanical and structural relations of MEMS are essential to assure the long-term functioning of devices, and have a significant impact on design and fabrication. Within this study a concept for the investigation of mechanically loaded MEMS materials on an atomic level is introduced, combining high-resolution X-ray diffraction (HRXRD) measurements with finite element analysis (FEA) and mechanical testing. In situ HRXRD measurements were performed on tensile loaded single crystal silicon (SCSi) specimens by means of profile scans and reciprocal space mapping (RSM) on symmetrical (004) and (440) reflections. A comprehensive evaluation of the rather complex XRD patterns and features was enabled by the correlation of measured with simulated, 'theoretical' patterns. Latter were calculated by a specifically developed, simple and fast approach on the basis of continuum mechanical relations. Qualitative and quantitative analysis confirmed the admissibility and accuracy of the presented method. In this context [001] Poisson's ratio was determined providing an error of less than 1.5% with respect to analytical prediction. Consequently, the introduced procedure contributes to further going investigations of weak scattering being related to strain and defects in crystalline structures and therefore supports investigations on materials and devices failure mechanisms.

Effective properties of dispersed phase reinforced composite materials with perfect and imperfect interfaces

NASA Astrophysics Data System (ADS)

Han, Ru

This thesis focuses on the analysis of dispersed phase reinforced composite materials with perfect as well as imperfect interfaces using the Boundary Element Method (BEM). Two problems of interest are considered, namely, to determine the limitations in the use of effective properties and the analysis of failure progression at the inclusion-matrix interface. The effective moduli (effective Young's modulus, effective Poisson's ratio, effective shear modulus, and effective bulk modulus) of composite materials can be determined at the mesoscopic level using three-dimensional parallel BEM simulations. By comparing the mesoscopic BEM results and the macroscopic results based on effective properties, limitations in the effective property approach can be determined. Decohesion is an important failure mode associated with fiber-reinforced composite materials. Analysis of failure progression at the fiber-matrix interface in fiber-reinforced composite materials is considered using a softening decohesion model consistent with thermodynamic concepts. In this model, the initiation of failure is given directly by a failure criterion. Damage is interpreted by the development of a discontinuity of displacement. The formulation describing the potential development of damage is governed by a discrete decohesive constitutive equation. Numerical simulations are performed using the direct boundary element method. Incremental decohesion simulations illustrate the progressive evolution of debonding zones and the propagation of cracks along the interfaces. The effect of decohesion on the macroscopic response of composite materials is also investigated.

Phased array inspection of large size forged steel parts

NASA Astrophysics Data System (ADS)

Dupont-Marillia, Frederic; Jahazi, Mohammad; Belanger, Pierre

2018-04-01

High strength forged steel requires uncompromising quality to warrant advance performance for numerous critical applications. Ultrasonic inspection is commonly used in nondestructive testing to detect cracks and other defects. In steel blocks of relatively small dimensions (at least two directions not exceeding a few centimetres), phased array inspection is a trusted method to generate images of the inside of the blocks and therefore identify and size defects. However, casting of large size forged ingots introduces changes of mechanical parameters such as grain size, the Young's modulus, the Poisson's ratio, and the chemical composition. These heterogeneities affect the wave propagation, and consequently, the reliability of ultrasonic inspection and the imaging capabilities for these blocks. In this context, a custom phased array transducer designed for a 40-ton bainitic forged ingot was investigated. Following a previous study that provided local mechanical parameters for a similar block, two-dimensional simulations were made to compute the optimal transducer parameters including the pitch, width and number of elements. It appeared that depending on the number of elements, backwall reconstruction can generate high amplitude artefacts. Indeed, the large dimensions of the simulated block introduce numerous constructive interferences from backwall reflections which may lead to important artefacts. To increase image quality, the reconstruction algorithm was adapted and promising results were observed and compared with the scattering cone filter method available in the CIVA software.

Poissonian renormalizations, exponentials, and power laws

NASA Astrophysics Data System (ADS)

Eliazar, Iddo

2013-05-01

This paper presents a comprehensive “renormalization study” of Poisson processes governed by exponential and power-law intensities. These Poisson processes are of fundamental importance, as they constitute the very bedrock of the universal extreme-value laws of Gumbel, Fréchet, and Weibull. Applying the method of Poissonian renormalization we analyze the emergence of these Poisson processes, unveil their intrinsic dynamical structures, determine their domains of attraction, and characterize their structural phase transitions. These structural phase transitions are shown to be governed by uniform and harmonic intensities, to have universal domains of attraction, to uniquely display intrinsic invariance, and to be intimately connected to “white noise” and to “1/f noise.” Thus, we establish a Poissonian explanation to the omnipresence of white and 1/f noises.

A new approach for handling longitudinal count data with zero-inflation and overdispersion: poisson geometric process model.

PubMed

Wan, Wai-Yin; Chan, Jennifer S K

2009-08-01

For time series of count data, correlated measurements, clustering as well as excessive zeros occur simultaneously in biomedical applications. Ignoring such effects might contribute to misleading treatment outcomes. A generalized mixture Poisson geometric process (GMPGP) model and a zero-altered mixture Poisson geometric process (ZMPGP) model are developed from the geometric process model, which was originally developed for modelling positive continuous data and was extended to handle count data. These models are motivated by evaluating the trend development of new tumour counts for bladder cancer patients as well as by identifying useful covariates which affect the count level. The models are implemented using Bayesian method with Markov chain Monte Carlo (MCMC) algorithms and are assessed using deviance information criterion (DIC).

Poisson statistics of PageRank probabilities of Twitter and Wikipedia networks

NASA Astrophysics Data System (ADS)

Frahm, Klaus M.; Shepelyansky, Dima L.

2014-04-01

We use the methods of quantum chaos and Random Matrix Theory for analysis of statistical fluctuations of PageRank probabilities in directed networks. In this approach the effective energy levels are given by a logarithm of PageRank probability at a given node. After the standard energy level unfolding procedure we establish that the nearest spacing distribution of PageRank probabilities is described by the Poisson law typical for integrable quantum systems. Our studies are done for the Twitter network and three networks of Wikipedia editions in English, French and German. We argue that due to absence of level repulsion the PageRank order of nearby nodes can be easily interchanged. The obtained Poisson law implies that the nearby PageRank probabilities fluctuate as random independent variables.

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

DTIC Science & Technology

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

Communication: modeling charge-sign asymmetric solvation free energies with nonlinear boundary conditions.

PubMed

Bardhan, Jaydeep P; Knepley, Matthew G

2014-10-07

We show that charge-sign-dependent asymmetric hydration can be modeled accurately using linear Poisson theory after replacing the standard electric-displacement boundary condition with a simple nonlinear boundary condition. Using a single multiplicative scaling factor to determine atomic radii from molecular dynamics Lennard-Jones parameters, the new model accurately reproduces MD free-energy calculations of hydration asymmetries for: (i) monatomic ions, (ii) titratable amino acids in both their protonated and unprotonated states, and (iii) the Mobley "bracelet" and "rod" test problems [D. L. Mobley, A. E. Barber II, C. J. Fennell, and K. A. Dill, "Charge asymmetries in hydration of polar solutes," J. Phys. Chem. B 112, 2405-2414 (2008)]. Remarkably, the model also justifies the use of linear response expressions for charging free energies. Our boundary-element method implementation demonstrates the ease with which other continuum-electrostatic solvers can be extended to include asymmetry.

Communication: Modeling charge-sign asymmetric solvation free energies with nonlinear boundary conditions

PubMed Central

Bardhan, Jaydeep P.; Knepley, Matthew G.

2014-01-01

We show that charge-sign-dependent asymmetric hydration can be modeled accurately using linear Poisson theory after replacing the standard electric-displacement boundary condition with a simple nonlinear boundary condition. Using a single multiplicative scaling factor to determine atomic radii from molecular dynamics Lennard-Jones parameters, the new model accurately reproduces MD free-energy calculations of hydration asymmetries for: (i) monatomic ions, (ii) titratable amino acids in both their protonated and unprotonated states, and (iii) the Mobley “bracelet” and “rod” test problems [D. L. Mobley, A. E. Barber II, C. J. Fennell, and K. A. Dill, “Charge asymmetries in hydration of polar solutes,” J. Phys. Chem. B 112, 2405–2414 (2008)]. Remarkably, the model also justifies the use of linear response expressions for charging free energies. Our boundary-element method implementation demonstrates the ease with which other continuum-electrostatic solvers can be extended to include asymmetry. PMID:25296776

Analytic analysis of auxetic metamaterials through analogy with rigid link systems

NASA Astrophysics Data System (ADS)

Rayneau-Kirkhope, Daniel; Zhang, Chengzhao; Theran, Louis; Dias, Marcelo A.

2018-02-01

In recent years, many structural motifs have been designed with the aim of creating auxetic metamaterials. One area of particular interest in this subject is the creation of auxetic material properties through elastic instability. Such metamaterials switch from conventional behaviour to an auxetic response for loads greater than some threshold value. This paper develops a novel methodology in the analysis of auxetic metamaterials which exhibit elastic instability through analogy with rigid link lattice systems. The results of our analytic approach are confirmed by finite-element simulations for both the onset of elastic instability and post-buckling behaviour including Poisson's ratio. The method gives insight into the relationships between mechanisms within lattices and their mechanical behaviour; as such, it has the potential to allow existing knowledge of rigid link lattices with auxetic paths to be used in the design of future buckling-induced auxetic metamaterials.

Radial basis functions in mathematical modelling of flow boiling in minichannels

NASA Astrophysics Data System (ADS)

Hożejowska, Sylwia; Hożejowski, Leszek; Piasecka, Magdalena

The paper addresses heat transfer processes in flow boiling in a vertical minichannel of 1.7 mm depth with a smooth heated surface contacting fluid. The heated element for FC-72 flowing in a minichannel was a 0.45 mm thick plate made of Haynes-230 alloy. An infrared camera positioned opposite the central, axially symmetric part of the channel measured the plate temperature. K-type thermocouples and pressure converters were installed at the inlet and outlet of the minichannel. In the study radial basis functions were used to solve a problem concerning heat transfer in a heated plate supplied with the controlled direct current. According to the model assumptions, the problem is treated as twodimensional and governed by the Poisson equation. The aim of the study lies in determining the temperature field and the heat transfer coefficient. The results were verified by comparing them with those obtained by the Trefftz method.

Hyperspectral image reconstruction for x-ray fluorescence tomography

DOE PAGES

Gürsoy, Doǧa; Biçer, Tekin; Lanzirotti, Antonio; ...

2015-01-01

A penalized maximum-likelihood estimation is proposed to perform hyperspectral (spatio-spectral) image reconstruction for X-ray fluorescence tomography. The approach minimizes a Poisson-based negative log-likelihood of the observed photon counts, and uses a penalty term that has the effect of encouraging local continuity of model parameter estimates in both spatial and spectral dimensions simultaneously. The performance of the reconstruction method is demonstrated with experimental data acquired from a seed of arabidopsis thaliana collected at the 13-ID-E microprobe beamline at the Advanced Photon Source. The resulting element distribution estimates with the proposed approach show significantly better reconstruction quality than the conventional analytical inversionmore » approaches, and allows for a high data compression factor which can reduce data acquisition times remarkably. In particular, this technique provides the capability to tomographically reconstruct full energy dispersive spectra without compromising reconstruction artifacts that impact the interpretation of results.« less

Numerical Study on Recombination Efficiency at 4,4'-Bis(2,2'-diphenylvinyl)-1,1'-spirobiphenyl/Tris(8-quinolinolato)aluminium Interface in Organic Light Emitting Diodes

NASA Astrophysics Data System (ADS)

Hwang, Young Wook; Kim, Kwang Sik; Won, Tae Young

2013-10-01

In this paper, we report our numerical study on the electrical and optical properties of the organic light emitting diodes (OLEDs) devices with n-doped layer, which is inserted for the purpose of reducing the interface barrier height between the cathode and the electron transport layer (ETL). We performed finite element method (FEM) simulation on OLEDs in order to understand the transport behavior of carriers, recombination kinetics, and emission property. Our model includes Poisson's equation, continuity equation to account for behavior of electrons and holes and exciton continuity/transfer equation to account for recombination of carriers. We employ the multilayer structure which consists of indium tin oxide (ITO); 2,2',7,7'-tetrakis(N,N-diphenylamine)-9,9'-spirobi-fluorene (S-TAD); 4,4'-bis(2,2'-diphenylvinyl)-1,1'-spirobiphenyl (S-DPVBi); tris(8-quinolinolato)aluminium (Alq3); calcium (Ca).

Classifying next-generation sequencing data using a zero-inflated Poisson model.

PubMed

Zhou, Yan; Wan, Xiang; Zhang, Baoxue; Tong, Tiejun

2018-04-15

With the development of high-throughput techniques, RNA-sequencing (RNA-seq) is becoming increasingly popular as an alternative for gene expression analysis, such as RNAs profiling and classification. Identifying which type of diseases a new patient belongs to with RNA-seq data has been recognized as a vital problem in medical research. As RNA-seq data are discrete, statistical methods developed for classifying microarray data cannot be readily applied for RNA-seq data classification. Witten proposed a Poisson linear discriminant analysis (PLDA) to classify the RNA-seq data in 2011. Note, however, that the count datasets are frequently characterized by excess zeros in real RNA-seq or microRNA sequence data (i.e. when the sequence depth is not enough or small RNAs with the length of 18-30 nucleotides). Therefore, it is desired to develop a new model to analyze RNA-seq data with an excess of zeros. In this paper, we propose a Zero-Inflated Poisson Logistic Discriminant Analysis (ZIPLDA) for RNA-seq data with an excess of zeros. The new method assumes that the data are from a mixture of two distributions: one is a point mass at zero, and the other follows a Poisson distribution. We then consider a logistic relation between the probability of observing zeros and the mean of the genes and the sequencing depth in the model. Simulation studies show that the proposed method performs better than, or at least as well as, the existing methods in a wide range of settings. Two real datasets including a breast cancer RNA-seq dataset and a microRNA-seq dataset are also analyzed, and they coincide with the simulation results that our proposed method outperforms the existing competitors. The software is available at http://www.math.hkbu.edu.hk/∼tongt. xwan@comp.hkbu.edu.hk or tongt@hkbu.edu.hk. Supplementary data are available at Bioinformatics online.

Analytical, numerical, and experimental investigations on effective mechanical properties and performances of carbon nanotubes and nanotube based nanocomposites with novel three dimensional nanostructures

NASA Astrophysics Data System (ADS)

Askari, Davood

The theoretical objectives and accomplishment of this work are the analytical and numerical investigation of material properties and mechanical behavior of carbon nanotubes (CNTs) and nanotube nanocomposites when they are subjected to various loading conditions. First, the finite element method is employed to investigate numerically the effective Young's modulus and Poisson's ratio of a single-walled CNT. Next, the effects of chirality on the effective Young's modulus and Poisson's ratio are investigated and then variations of their effective coefficient of thermal expansions and effective thermal conductivities are studied for CNTs with different structural configurations. To study the influence of small vacancy defects on mechanical properties of CNTs, finite element analyses are performed and the behavior of CNTs with various structural configurations having different types of vacancy defects is studied. It is frequently reported that nano-materials are excellent candidates as reinforcements in nanocomposites to change or enhance material properties of polymers and their nanocomposites. Second, the inclusion of nano-materials can considerably improve electrical, thermal, and mechanical properties of the bonding agent, i.e., resin. Note that, materials atomic and molecular level do not usually show isotropic behaviour, rather they have orthotropic properties. Therefore, two-phase and three-phase cylindrically orthotropic composite models consisting of different constituents with orthotropic properties are developed and introduced in this work to analytically predict the effective mechanical properties and mechanical behavior of such structures when they are subjected to various external loading conditions. To verify the analytically obtained exact solutions, finite element analyses of identical cylindrical structures are also performed and then results are compared with those obtained analytically, and excellent agreement is achieved. The third part of this dissertation investigates the growth of vertically aligned, long, and high density arrays of CNTs and novel 3-D carbon nanotube nano-forests. A Chemical vapor deposition technique is used to grow radially aligned CNTs on various types of fibrous materials such as silicon carbide, carbon, Kevlar, and glass fibers and clothes that can be used for the fabrication of multifunctional high performing laminated nanocomposite structures. Using the CNTs nano-forest clothes, nanocomposite samples are prepared and tested giving promising results for the improvement of mechanical properties and performance of composites structures.

Binomial leap methods for simulating stochastic chemical kinetics.

PubMed

Tian, Tianhai; Burrage, Kevin

2004-12-01

This paper discusses efficient simulation methods for stochastic chemical kinetics. Based on the tau-leap and midpoint tau-leap methods of Gillespie [D. T. Gillespie, J. Chem. Phys. 115, 1716 (2001)], binomial random variables are used in these leap methods rather than Poisson random variables. The motivation for this approach is to improve the efficiency of the Poisson leap methods by using larger stepsizes. Unlike Poisson random variables whose range of sample values is from zero to infinity, binomial random variables have a finite range of sample values. This probabilistic property has been used to restrict possible reaction numbers and to avoid negative molecular numbers in stochastic simulations when larger stepsize is used. In this approach a binomial random variable is defined for a single reaction channel in order to keep the reaction number of this channel below the numbers of molecules that undergo this reaction channel. A sampling technique is also designed for the total reaction number of a reactant species that undergoes two or more reaction channels. Samples for the total reaction number are not greater than the molecular number of this species. In addition, probability properties of the binomial random variables provide stepsize conditions for restricting reaction numbers in a chosen time interval. These stepsize conditions are important properties of robust leap control strategies. Numerical results indicate that the proposed binomial leap methods can be applied to a wide range of chemical reaction systems with very good accuracy and significant improvement on efficiency over existing approaches. (c) 2004 American Institute of Physics.

Statistical error in simulations of Poisson processes: Example of diffusion in solids

NASA Astrophysics Data System (ADS)

Nilsson, Johan O.; Leetmaa, Mikael; Vekilova, Olga Yu.; Simak, Sergei I.; Skorodumova, Natalia V.

2016-08-01

Simulations of diffusion in solids often produce poor statistics of diffusion events. We present an analytical expression for the statistical error in ion conductivity obtained in such simulations. The error expression is not restricted to any computational method in particular, but valid in the context of simulation of Poisson processes in general. This analytical error expression is verified numerically for the case of Gd-doped ceria by running a large number of kinetic Monte Carlo calculations.

Fractional Brownian motion and long term clinical trial recruitment

PubMed Central

Zhang, Qiang; Lai, Dejian

2015-01-01

Prediction of recruitment in clinical trials has been a challenging task. Many methods have been studied, including models based on Poisson process and its large sample approximation by Brownian motion (BM), however, when the independent incremental structure is violated for BM model, we could use fractional Brownian motion to model and approximate the underlying Poisson processes with random rates. In this paper, fractional Brownian motion (FBM) is considered for such conditions and compared to BM model with illustrated examples from different trials and simulations. PMID:26347306

Fractional Brownian motion and long term clinical trial recruitment.

PubMed

Zhang, Qiang; Lai, Dejian

2011-05-01

Prediction of recruitment in clinical trials has been a challenging task. Many methods have been studied, including models based on Poisson process and its large sample approximation by Brownian motion (BM), however, when the independent incremental structure is violated for BM model, we could use fractional Brownian motion to model and approximate the underlying Poisson processes with random rates. In this paper, fractional Brownian motion (FBM) is considered for such conditions and compared to BM model with illustrated examples from different trials and simulations.

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

NASA Technical Reports Server (NTRS)

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

1995-01-01

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

A high order semi-Lagrangian discontinuous Galerkin method for Vlasov-Poisson simulations without operator splitting

NASA Astrophysics Data System (ADS)

Cai, Xiaofeng; Guo, Wei; Qiu, Jing-Mei

2018-02-01

In this paper, we develop a high order semi-Lagrangian (SL) discontinuous Galerkin (DG) method for nonlinear Vlasov-Poisson (VP) simulations without operator splitting. In particular, we combine two recently developed novel techniques: one is the high order non-splitting SLDG transport method (Cai et al. (2017) [4]), and the other is the high order characteristics tracing technique proposed in Qiu and Russo (2017) [29]. The proposed method with up to third order accuracy in both space and time is locally mass conservative, free of splitting error, positivity-preserving, stable and robust for large time stepping size. The SLDG VP solver is applied to classic benchmark test problems such as Landau damping and two-stream instabilities for VP simulations. Efficiency and effectiveness of the proposed scheme is extensively tested. Tremendous CPU savings are shown by comparisons between the proposed SL DG scheme and the classical Runge-Kutta DG method.

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

Finding consistent patterns: A nonparametric approach for identifying differential expression in RNA-Seq data

PubMed Central

Li, Jun; Tibshirani, Robert

2015-01-01

We discuss the identification of features that are associated with an outcome in RNA-Sequencing (RNA-Seq) and other sequencing-based comparative genomic experiments. RNA-Seq data takes the form of counts, so models based on the normal distribution are generally unsuitable. The problem is especially challenging because different sequencing experiments may generate quite different total numbers of reads, or ‘sequencing depths’. Existing methods for this problem are based on Poisson or negative binomial models: they are useful but can be heavily influenced by ‘outliers’ in the data. We introduce a simple, nonparametric method with resampling to account for the different sequencing depths. The new method is more robust than parametric methods. It can be applied to data with quantitative, survival, two-class or multiple-class outcomes. We compare our proposed method to Poisson and negative binomial-based methods in simulated and real data sets, and find that our method discovers more consistent patterns than competing methods. PMID:22127579

An analytic model for accurate spring constant calibration of rectangular atomic force microscope cantilevers.

PubMed

Li, Rui; Ye, Hongfei; Zhang, Weisheng; Ma, Guojun; Su, Yewang

2015-10-29

Spring constant calibration of the atomic force microscope (AFM) cantilever is of fundamental importance for quantifying the force between the AFM cantilever tip and the sample. The calibration within the framework of thin plate theory undoubtedly has a higher accuracy and broader scope than that within the well-established beam theory. However, thin plate theory-based accurate analytic determination of the constant has been perceived as an extremely difficult issue. In this paper, we implement the thin plate theory-based analytic modeling for the static behavior of rectangular AFM cantilevers, which reveals that the three-dimensional effect and Poisson effect play important roles in accurate determination of the spring constants. A quantitative scaling law is found that the normalized spring constant depends only on the Poisson's ratio, normalized dimension and normalized load coordinate. Both the literature and our refined finite element model validate the present results. The developed model is expected to serve as the benchmark for accurate calibration of rectangular AFM cantilevers.

Likelihood inference for COM-Poisson cure rate model with interval-censored data and Weibull lifetimes.

PubMed

Pal, Suvra; Balakrishnan, N

2017-10-01

In this paper, we consider a competing cause scenario and assume the number of competing causes to follow a Conway-Maxwell Poisson distribution which can capture both over and under dispersion that is usually encountered in discrete data. Assuming the population of interest having a component cure and the form of the data to be interval censored, as opposed to the usually considered right-censored data, the main contribution is in developing the steps of the expectation maximization algorithm for the determination of the maximum likelihood estimates of the model parameters of the flexible Conway-Maxwell Poisson cure rate model with Weibull lifetimes. An extensive Monte Carlo simulation study is carried out to demonstrate the performance of the proposed estimation method. Model discrimination within the Conway-Maxwell Poisson distribution is addressed using the likelihood ratio test and information-based criteria to select a suitable competing cause distribution that provides the best fit to the data. A simulation study is also carried out to demonstrate the loss in efficiency when selecting an improper competing cause distribution which justifies the use of a flexible family of distributions for the number of competing causes. Finally, the proposed methodology and the flexibility of the Conway-Maxwell Poisson distribution are illustrated with two known data sets from the literature: smoking cessation data and breast cosmesis data.

SIERRA - A 3-D device simulator for reliability modeling

NASA Astrophysics Data System (ADS)

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

1989-05-01

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

Safety assessment of a shallow foundation using the random finite element method

NASA Astrophysics Data System (ADS)

Zaskórski, Łukasz; Puła, Wojciech

2015-04-01

A complex structure of soil and its random character are reasons why soil modeling is a cumbersome task. Heterogeneity of soil has to be considered even within a homogenous layer of soil. Therefore an estimation of shear strength parameters of soil for the purposes of a geotechnical analysis causes many problems. In applicable standards (Eurocode 7) there is not presented any explicit method of an evaluation of characteristic values of soil parameters. Only general guidelines can be found how these values should be estimated. Hence many approaches of an assessment of characteristic values of soil parameters are presented in literature and can be applied in practice. In this paper, the reliability assessment of a shallow strip footing was conducted using a reliability index β. Therefore some approaches of an estimation of characteristic values of soil properties were compared by evaluating values of reliability index β which can be achieved by applying each of them. Method of Orr and Breysse, Duncan's method, Schneider's method, Schneider's method concerning influence of fluctuation scales and method included in Eurocode 7 were examined. Design values of the bearing capacity based on these approaches were referred to the stochastic bearing capacity estimated by the random finite element method (RFEM). Design values of the bearing capacity were conducted for various widths and depths of a foundation in conjunction with design approaches DA defined in Eurocode. RFEM was presented by Griffiths and Fenton (1993). It combines deterministic finite element method, random field theory and Monte Carlo simulations. Random field theory allows to consider a random character of soil parameters within a homogenous layer of soil. For this purpose a soil property is considered as a separate random variable in every element of a mesh in the finite element method with proper correlation structure between points of given area. RFEM was applied to estimate which theoretical probability distribution fits the empirical probability distribution of bearing capacity basing on 3000 realizations. Assessed probability distribution was applied to compute design values of the bearing capacity and related reliability indices β. Conducted analysis were carried out for a cohesion soil. Hence a friction angle and a cohesion were defined as a random parameters and characterized by two dimensional random fields. A friction angle was described by a bounded distribution as it differs within limited range. While a lognormal distribution was applied in case of a cohesion. Other properties - Young's modulus, Poisson's ratio and unit weight were assumed as deterministic values because they have negligible influence on the stochastic bearing capacity. Griffiths D. V., & Fenton G. A. (1993). Seepage beneath water retaining structures founded on spatially random soil. Géotechnique, 43(6), 577-587.

Properties of the Bivariate Delayed Poisson Process

DTIC Science & Technology

1974-07-01

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

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

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.

Exploring spatial patterns of sudden cardiac arrests in the city of Toronto using Poisson kriging and Hot Spot analyses.

PubMed

Przybysz, Raymond; Bunch, Martin

2017-01-01

Our study looked at out-of-hospital sudden cardiac arrest events in the City of Toronto. These are relatively rare events, yet present a serious global clinical and public health problem. We report on the application of spatial methods and tools that, although relatively well known to geographers and natural resource scientists, need to become better known and used more frequently by health care researchers. Our data came from the population-based Rescu Epistry cardiac arrest database. We limited it to the residents of the City of Toronto who experienced sudden arrest in 2010. The data was aggregated at the Dissemination Area level, and population rates were calculated. Poisson kriging was carried out on one year of data using three different spatial weights. Kriging estimates were then compared in Hot Spot analyses. Spatial analysis revealed that Poisson kriging can yield reliable rates using limited data of high quality. We observed the highest rates of sudden arrests in the north and central parts of Etobicoke, western parts of North York as well as the central and southwestern parts of Scarborough while the lowest rates were found in north and eastern parts of Scarborough, downtown Toronto, and East York as well as east central parts of North York. Influence of spatial neighbours on the results did not extend past two rings of adjacent units. Poisson kriging has the potential to be applied to a wide range of healthcare research, particularly on rare events. This approach can be successfully combined with other spatial methods. More applied research, is needed to establish a wider acceptance for this method, especially among healthcare researchers and epidemiologists.

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

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

Gonis, Antonios; Zhang, Xiaoguang

2012-01-01

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

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

NASA Astrophysics Data System (ADS)

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

2012-09-01

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

A mixed method Poisson solver for three-dimensional self-gravitating astrophysical fluid dynamical systems

NASA Technical Reports Server (NTRS)

Duncan, Comer; Jones, Jim

1993-01-01

A key ingredient in the simulation of self-gravitating astrophysical fluid dynamical systems is the gravitational potential and its gradient. This paper focuses on the development of a mixed method multigrid solver of the Poisson equation formulated so that both the potential and the Cartesian components of its gradient are self-consistently and accurately generated. The method achieves this goal by formulating the problem as a system of four equations for the gravitational potential and the three Cartesian components of the gradient and solves them using a distributed relaxation technique combined with conventional full multigrid V-cycles. The method is described, some tests are presented, and the accuracy of the method is assessed. We also describe how the method has been incorporated into our three-dimensional hydrodynamics code and give an example of an application to the collision of two stars. We end with some remarks about the future developments of the method and some of the applications in which it will be used in astrophysics.

Boundary Layer Effect on Behavior of Discrete Models.

PubMed

Eliáš, Jan

2017-02-10

The paper studies systems of rigid bodies with randomly generated geometry interconnected by normal and tangential bonds. The stiffness of these bonds determines the macroscopic elastic modulus while the macroscopic Poisson's ratio of the system is determined solely by the normal/tangential stiffness ratio. Discrete models with no directional bias have the same probability of element orientation for any direction and therefore the same mechanical properties in a statistical sense at any point and direction. However, the layers of elements in the vicinity of the boundary exhibit biased orientation, preferring elements parallel with the boundary. As a consequence, when strain occurs in this direction, the boundary layer becomes stiffer than the interior for the normal/tangential stiffness ratio larger than one, and vice versa. Nonlinear constitutive laws are typically such that the straining of an element in shear results in higher strength and ductility than straining in tension. Since the boundary layer tends, due to the bias in the elemental orientation, to involve more tension than shear at the contacts, it also becomes weaker and less ductile. The paper documents these observations and compares them to the results of theoretical analysis.

[Downscaling research of spatial distribution of incidence of hand foot and mouth disease based on area-to-area Poisson Kriging method].

PubMed

Wang, J X; Hu, M G; Yu, S C; Xiao, G X

2017-09-10

Objective: To understand the spatial distribution of incidence of hand foot and mouth disease (HFMD) at scale of township and provide evidence for the better prevention and control of HFMD and allocation of medical resources. Methods: The incidence data of HFMD in 108 counties (district) in Shandong province in 2010 were collected. Downscaling interpolation was conducted by using area-to-area Poisson Kriging method. The interpolation results were visualized by using geographic information system (GIS). The county (district) incidence was interpolated into township incidence to get the distribution of spatial distribution of incidence of township. Results: In the downscaling interpolation, the range of the fitting semi-variance equation was 20.38 km. Within the range, the incidence had correlation with each other. The fitting function of scatter diagram of estimated and actual incidence of HFMD at country level was y =1.053 1 x , R (2)=0.99. The incidences at different scale were consistent. Conclusions: The incidence of HFMD had spatial autocorrelation within 20.38 km. When HFMD occurs in one place, it is necessary to strengthen the surveillance and allocation of medical resource in the surrounding area within 20.38 km. Area to area Poisson Kriging method based downscaling research can be used in spatial visualization of HFMD incidence.

Orientational analysis of planar fibre systems observed as a Poisson shot-noise process.

PubMed

Kärkkäinen, Salme; Lantuéjoul, Christian

2007-10-01

We consider two-dimensional fibrous materials observed as a digital greyscale image. The problem addressed is to estimate the orientation distribution of unobservable thin fibres from a greyscale image modelled by a planar Poisson shot-noise process. The classical stereological approach is not straightforward, because the point intensities of thin fibres along sampling lines may not be observable. For such cases, Kärkkäinen et al. (2001) suggested the use of scaled variograms determined from grey values along sampling lines in several directions. Their method is based on the assumption that the proportion between the scaled variograms and point intensities in all directions of sampling lines is constant. This assumption is proved to be valid asymptotically for Boolean models and dead leaves models, under some regularity conditions. In this work, we derive the scaled variogram and its approximations for a planar Poisson shot-noise process using the modified Bessel function. In the case of reasonable high resolution of the observed image, the scaled variogram has an approximate functional relation to the point intensity, and in the case of high resolution the relation is proportional. As the obtained relations are approximative, they are tested on simulations. The existing orientation analysis method based on the proportional relation is further experimented on images with different resolutions. The new result, the asymptotic proportionality between the scaled variograms and the point intensities for a Poisson shot-noise process, completes the earlier results for the Boolean models and for the dead leaves models.

Simultaneous measurement of the Young's modulus and the Poisson ratio of thin elastic layers.

PubMed

Gross, Wolfgang; Kress, Holger

2017-02-07

The behavior of cells and tissue is greatly influenced by the mechanical properties of their environment. For studies on the interactions between cells and soft matrices, especially those applying traction force microscopy the characterization of the mechanical properties of thin substrate layers is essential. Various techniques to measure the elastic modulus are available. Methods to accurately measure the Poisson ratio of such substrates are rare and often imply either a combination of multiple techniques or additional equipment which is not needed for the actual biological studies. Here we describe a novel technique to measure both parameters, the Youngs's modulus and the Poisson ratio in a single experiment. The technique requires only a standard inverted epifluorescence microscope. As a model system, we chose cross-linked polyacrylamide and poly-N-isopropylacrylamide hydrogels which are known to obey Hooke's law. We place millimeter-sized steel spheres on the substrates which indent the surface. The data are evaluated using a previously published model which takes finite thickness effects of the substrate layer into account. We demonstrate experimentally for the first time that the application of the model allows the simultaneous determination of both the Young's modulus and the Poisson ratio. Since the method is easy to adapt and comes without the need of special equipment, we envision the technique to become a standard tool for the characterization of substrates for a wide range of investigations of cell and tissue behavior in various mechanical environments as well as other samples, including biological materials.

Methodology for extraction of space charge density profiles at nanoscale from Kelvin probe force microscopy measurements.

PubMed

Villeneuve-Faure, C; Boudou, L; Makasheva, K; Teyssedre, G

2017-12-15

To understand the physical phenomena occurring at metal/dielectric interfaces, determination of the charge density profile at nanoscale is crucial. To deal with this issue, charges were injected applying a DC voltage on lateral Al-electrodes embedded in a SiN x thin dielectric layer. The surface potential induced by the injected charges was probed by Kelvin probe force microscopy (KPFM). It was found that the KPFM frequency mode is a better adapted method to probe accurately the charge profile. To extract the charge density profile from the surface potential two numerical approaches based on the solution to Poisson's equation for electrostatics were investigated: the second derivative model method, already reported in the literature, and a new 2D method based on the finite element method (FEM). Results highlight that the FEM is more robust to noise or artifacts in the case of a non-flat initial surface potential. Moreover, according to theoretical study the FEM appears to be a good candidate for determining charge density in dielectric films with thicknesses in the range from 10 nm to 10 μm. By applying this method, the charge density profile was determined at nanoscale, highlighting that the charge cloud remains close to the interface.

Asteroid families - An initial search

NASA Technical Reports Server (NTRS)

Williams, James G.

1992-01-01

A stereo examination was conducted for clusters in three-dimensional proper element space within a sample of both numbered and faint Palomar-Leiden Survey (PLS) asteroids. The clusters were then objectively filtered for small Poisson probability of chance occurrence; 104 were accepted as families with 4- to 12-member populations, and are interpreted as impact-generated. Structure is common in the well-populated families: the better-sampled families are accordingly discussed in terms of their geometry and taxonomy. Some families are very rich in faint PLS members.

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.

Evaluating Micrometeoroid and Orbital Debris Risk Assessments Using Anomaly Data

NASA Technical Reports Server (NTRS)

Squire, Michael

2017-01-01

The accuracy of micrometeoroid and orbital debris (MMOD) risk assessments can be difficult to evaluate. A team from the National Aeronautics and Space Administration (NASA) Engineering and Safety Center (NESC) has completed a study that compared MMOD-related failures on operational satellites to predictions of how many of those failures should occur using NASA's TM"s MMOD risk assessment methodology and tools. The study team used the Poisson probability to quantify the degree of inconsistency between the predicted and reported numbers of failures. Many elements go into a risk assessment, and each of those elements represent a possible source of uncertainty or bias that will influence the end result. There are also challenges in obtaining accurate and useful data on MMOD-related failures.

A software platform for continuum modeling of ion channels based on unstructured mesh

NASA Astrophysics Data System (ADS)

Tu, B.; Bai, S. Y.; Chen, M. X.; Xie, Y.; Zhang, L. B.; Lu, B. Z.

2014-01-01

Most traditional continuum molecular modeling adopted finite difference or finite volume methods which were based on a structured mesh (grid). Unstructured meshes were only occasionally used, but an increased number of applications emerge in molecular simulations. To facilitate the continuum modeling of biomolecular systems based on unstructured meshes, we are developing a software platform with tools which are particularly beneficial to those approaches. This work describes the software system specifically for the simulation of a typical, complex molecular procedure: ion transport through a three-dimensional channel system that consists of a protein and a membrane. The platform contains three parts: a meshing tool chain for ion channel systems, a parallel finite element solver for the Poisson-Nernst-Planck equations describing the electrodiffusion process of ion transport, and a visualization program for continuum molecular modeling. The meshing tool chain in the platform, which consists of a set of mesh generation tools, is able to generate high-quality surface and volume meshes for ion channel systems. The parallel finite element solver in our platform is based on the parallel adaptive finite element package PHG which wass developed by one of the authors [1]. As a featured component of the platform, a new visualization program, VCMM, has specifically been developed for continuum molecular modeling with an emphasis on providing useful facilities for unstructured mesh-based methods and for their output analysis and visualization. VCMM provides a graphic user interface and consists of three modules: a molecular module, a meshing module and a numerical module. A demonstration of the platform is provided with a study of two real proteins, the connexin 26 and hemolysin ion channels.

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

NASA Astrophysics Data System (ADS)

Exl, Lukas

2017-12-01

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

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.

High order multi-grid methods to solve the Poisson equation

NASA Technical Reports Server (NTRS)

Schaffer, S.

1981-01-01

High order multigrid methods based on finite difference discretization of the model problem are examined. The following methods are described: (1) a fixed high order FMG-FAS multigrid algorithm; (2) the high order methods; and (3) results are presented on four problems using each method with the same underlying fixed FMG-FAS algorithm.

CCM Continuity Constraint Method: A finite-element computational fluid dynamics algorithm for incompressible Navier-Stokes fluid flows

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

Williams, P. T.

1993-09-01

As the field of computational fluid dynamics (CFD) continues to mature, algorithms are required to exploit the most recent advances in approximation theory, numerical mathematics, computing architectures, and hardware. Meeting this requirement is particularly challenging in incompressible fluid mechanics, where primitive-variable CFD formulations that are robust, while also accurate and efficient in three dimensions, remain an elusive goal. This dissertation asserts that one key to accomplishing this goal is recognition of the dual role assumed by the pressure, i.e., a mechanism for instantaneously enforcing conservation of mass and a force in the mechanical balance law for conservation of momentum. Provingmore » this assertion has motivated the development of a new, primitive-variable, incompressible, CFD algorithm called the Continuity Constraint Method (CCM). The theoretical basis for the CCM consists of a finite-element spatial semi-discretization of a Galerkin weak statement, equal-order interpolation for all state-variables, a 0-implicit time-integration scheme, and a quasi-Newton iterative procedure extended by a Taylor Weak Statement (TWS) formulation for dispersion error control. Original contributions to algorithmic theory include: (a) formulation of the unsteady evolution of the divergence error, (b) investigation of the role of non-smoothness in the discretized continuity-constraint function, (c) development of a uniformly H 1 Galerkin weak statement for the Reynolds-averaged Navier-Stokes pressure Poisson equation, (d) derivation of physically and numerically well-posed boundary conditions, and (e) investigation of sparse data structures and iterative methods for solving the matrix algebra statements generated by the algorithm.« less

Efficiency of perfectly matched layers for seismic wave modeling in second-order viscoelastic equations

NASA Astrophysics Data System (ADS)

Ping, Ping; Zhang, Yu; Xu, Yixian; Chu, Risheng

2016-12-01

In order to improve the perfectly matched layer (PML) efficiency in viscoelastic media, we first propose a split multi-axial PML (M-PML) and an unsplit convolutional PML (C-PML) in the second-order viscoelastic wave equations with the displacement as the only unknown. The advantage of these formulations is that it is easy and efficient to revise the existing codes of the second-order spectral element method (SEM) or finite-element method (FEM) with absorbing boundaries in a uniform equation, as well as more economical than the auxiliary differential equations PML. Three models which are easily suffered from late time instabilities are considered to validate our approaches. Through comparison the M-PML with C-PML efficiency of absorption and stability for long time simulation, it can be concluded that: (1) for an isotropic viscoelastic medium with high Poisson's ratio, the C-PML will be a sufficient choice for long time simulation because of its weak reflections and superior stability; (2) unlike the M-PML with high-order damping profile, the M-PML with second-order damping profile loses its stability in long time simulation for an isotropic viscoelastic medium; (3) in an anisotropic viscoelastic medium, the C-PML suffers from instabilities, while the M-PML with second-order damping profile can be a better choice for its superior stability and more acceptable weak reflections than the M-PML with high-order damping profile. The comparative analysis of the developed methods offers meaningful significance for long time seismic wave modeling in second-order viscoelastic wave equations.

Muscle Activity Map Reconstruction from High Density Surface EMG Signals With Missing Channels Using Image Inpainting and Surface Reconstruction Methods.

PubMed

Ghaderi, Parviz; Marateb, Hamid R

2017-07-01

The aim of this study was to reconstruct low-quality High-density surface EMG (HDsEMG) signals, recorded with 2-D electrode arrays, using image inpainting and surface reconstruction methods. It is common that some fraction of the electrodes may provide low-quality signals. We used variety of image inpainting methods, based on partial differential equations (PDEs), and surface reconstruction methods to reconstruct the time-averaged or instantaneous muscle activity maps of those outlier channels. Two novel reconstruction algorithms were also proposed. HDsEMG signals were recorded from the biceps femoris and brachial biceps muscles during low-to-moderate-level isometric contractions, and some of the channels (5-25%) were randomly marked as outliers. The root-mean-square error (RMSE) between the original and reconstructed maps was then calculated. Overall, the proposed Poisson and wave PDE outperformed the other methods (average RMSE 8.7 μV rms ± 6.1 μV rms and 7.5 μV rms ± 5.9 μV rms ) for the time-averaged single-differential and monopolar map reconstruction, respectively. Biharmonic Spline, the discrete cosine transform, and the Poisson PDE outperformed the other methods for the instantaneous map reconstruction. The running time of the proposed Poisson and wave PDE methods, implemented using a Vectorization package, was 4.6 ± 5.7 ms and 0.6 ± 0.5 ms, respectively, for each signal epoch or time sample in each channel. The proposed reconstruction algorithms could be promising new tools for reconstructing muscle activity maps in real-time applications. Proper reconstruction methods could recover the information of low-quality recorded channels in HDsEMG signals.

Simulation methods with extended stability for stiff biochemical Kinetics.

PubMed

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

2010-08-11

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

Study of non-Hodgkin's lymphoma mortality associated with industrial pollution in Spain, using Poisson models

PubMed Central

Ramis, Rebeca; Vidal, Enrique; García-Pérez, Javier; Lope, Virginia; Aragonés, Nuria; Pérez-Gómez, Beatriz; Pollán, Marina; López-Abente, Gonzalo

2009-01-01

Background Non-Hodgkin's lymphomas (NHLs) have been linked to proximity to industrial areas, but evidence regarding the health risk posed by residence near pollutant industries is very limited. The European Pollutant Emission Register (EPER) is a public register that furnishes valuable information on industries that release pollutants to air and water, along with their geographical location. This study sought to explore the relationship between NHL mortality in small areas in Spain and environmental exposure to pollutant emissions from EPER-registered industries, using three Poisson-regression-based mathematical models. Methods Observed cases were drawn from mortality registries in Spain for the period 1994–2003. Industries were grouped into the following sectors: energy; metal; mineral; organic chemicals; waste; paper; food; and use of solvents. Populations having an industry within a radius of 1, 1.5, or 2 kilometres from the municipal centroid were deemed to be exposed. Municipalities outside those radii were considered as reference populations. The relative risks (RRs) associated with proximity to pollutant industries were estimated using the following methods: Poisson Regression; mixed Poisson model with random provincial effect; and spatial autoregressive modelling (BYM model). Results Only proximity of paper industries to population centres (>2 km) could be associated with a greater risk of NHL mortality (mixed model: RR:1.24, 95% CI:1.09–1.42; BYM model: RR:1.21, 95% CI:1.01–1.45; Poisson model: RR:1.16, 95% CI:1.06–1.27). Spatial models yielded higher estimates. Conclusion The reported association between exposure to air pollution from the paper, pulp and board industry and NHL mortality is independent of the model used. Inclusion of spatial random effects terms in the risk estimate improves the study of associations between environmental exposures and mortality. The EPER could be of great utility when studying the effects of industrial pollution on the health of the population. PMID:19159450

MO-G-17A-05: PET Image Deblurring Using Adaptive Dictionary Learning

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

Valiollahzadeh, S; Clark, J; Mawlawi, O

2014-06-15

Purpose: The aim of this work is to deblur PET images while suppressing Poisson noise effects using adaptive dictionary learning (DL) techniques. Methods: The model that relates a blurred and noisy PET image to the desired image is described as a linear transform y=Hm+n where m is the desired image, H is a blur kernel, n is Poisson noise and y is the blurred image. The approach we follow to recover m involves the sparse representation of y over a learned dictionary, since the image has lots of repeated patterns, edges, textures and smooth regions. The recovery is based onmore » an optimization of a cost function having four major terms: adaptive dictionary learning term, sparsity term, regularization term, and MLEM Poisson noise estimation term. The optimization is solved by a variable splitting method that introduces additional variables. We simulated a 128×128 Hoffman brain PET image (baseline) with varying kernel types and sizes (Gaussian 9×9, σ=5.4mm; Uniform 5×5, σ=2.9mm) with additive Poisson noise (Blurred). Image recovery was performed once when the kernel type was included in the model optimization and once with the model blinded to kernel type. The recovered image was compared to the baseline as well as another recovery algorithm PIDSPLIT+ (Setzer et. al.) by calculating PSNR (Peak SNR) and normalized average differences in pixel intensities (NADPI) of line profiles across the images. Results: For known kernel types, the PSNR of the Gaussian (Uniform) was 28.73 (25.1) and 25.18 (23.4) for DL and PIDSPLIT+ respectively. For blinded deblurring the PSNRs were 25.32 and 22.86 for DL and PIDSPLIT+ respectively. NADPI between baseline and DL, and baseline and blurred for the Gaussian kernel was 2.5 and 10.8 respectively. Conclusion: PET image deblurring using dictionary learning seems to be a good approach to restore image resolution in presence of Poisson noise. GE Health Care.« less

Crystalline nucleation in undercooled liquids: a Bayesian data-analysis approach for a nonhomogeneous Poisson process.

PubMed

Filipponi, A; Di Cicco, A; Principi, E

2012-12-01

A Bayesian data-analysis approach to data sets of maximum undercooling temperatures recorded in repeated melting-cooling cycles of high-purity samples is proposed. The crystallization phenomenon is described in terms of a nonhomogeneous Poisson process driven by a temperature-dependent sample nucleation rate J(T). The method was extensively tested by computer simulations and applied to real data for undercooled liquid Ge. It proved to be particularly useful in the case of scarce data sets where the usage of binned data would degrade the available experimental information.

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

A systematic typology for negative Poisson's ratio materials and the prediction of complete auxeticity in pure silica zeolite JST.

PubMed

Siddorn, M; Coudert, F-X; Evans, K E; Marmier, A

2015-07-21

Single crystals can commonly have negative Poisson's ratio in a few directions; however more generalised auxeticity is rarer. We propose a typology to distinguish auxetic materials. We characterise numerous single crystals and demonstrate that partial auxeticity occurs for around 37%. We find average auxeticity to be limited to α-cristobalite and no example of complete auxeticity. We simulate two hundreds pure silica zeolites with empirical potentials and quantum chemistry methods, and for the first time identify complete auxeticity in a zeolite network, JST.

Fission meter and neutron detection using poisson distribution comparison

DOEpatents

Rowland, Mark S; Snyderman, Neal J

2014-11-18

A neutron detector system and method for discriminating fissile material from non-fissile material wherein a digital data acquisition unit collects data at high rate, and in real-time processes large volumes of data directly into information that a first responder can use to discriminate materials. The system comprises counting neutrons from the unknown source and detecting excess grouped neutrons to identify fission in the unknown source. Comparison of the observed neutron count distribution with a Poisson distribution is performed to distinguish fissile material from non-fissile material.

Fractional Poisson Fields and Martingales

NASA Astrophysics Data System (ADS)

Aletti, Giacomo; Leonenko, Nikolai; Merzbach, Ely

2018-02-01

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

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

NASA Astrophysics Data System (ADS)

Chekhov, L. O.; Mazzocco, M.

2017-12-01

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

Elastic moduli of cast Ti-Au, Ti-Ag, and Ti-Cu alloys.

PubMed

Kikuchi, Masafumi; Takahashi, Masatoshi; Okuno, Osamu

2006-07-01

This study investigated the effect of alloying titanium with gold, silver, or copper on the elastic properties of the alloys. A series of binary titanium alloys was made with four concentrations of gold, silver, or copper (5, 10, 20, and 30 mass%) in an argon-arc melting furnace. The Young's moduli and Poisson's ratios of the alloy castings were determined with an ultrasonic-pulse method. The density of each alloy was previously measured by the Archimedes' principle. Results were analyzed using one-way ANOVA and the Scheffé's test. The densities of Ti-Au, Ti-Ag, and Ti-Cu alloys monotonically increased as the concentration of alloying elements increased. As the concentration of gold or silver increased to 20%, the Young's modulus significantly decreased, followed by a subsequent increase in value. As the concentration of copper increased, the Young's modulus monotonically increased. The Young's moduli of all the Ti-Cu alloys were significantly higher than that of the titanium. The density of all the experimental alloys was virtually independent of the alloy phases, while the Young's moduli and Poisson's ratios of the alloys were dependent. The addition of gold or silver slightly reduced the Young's modulus of the titanium when the alloy phase was single alpha. The increase in the Young's modulus of the Ti-Cu alloys is probably due to the precipitation of intermetallic compound Ti2Cu. Copper turned out to be a moderate stiffener that gains a Young's modulus of titanium up to 20% at the copper concentration of 30 mass%.

The contribution of simple random sampling to observed variations in faecal egg counts.

PubMed

Torgerson, Paul R; Paul, Michaela; Lewis, Fraser I

2012-09-10

It has been over 100 years since the classical paper published by Gosset in 1907, under the pseudonym "Student", demonstrated that yeast cells suspended in a fluid and measured by a haemocytometer conformed to a Poisson process. Similarly parasite eggs in a faecal suspension also conform to a Poisson process. Despite this there are common misconceptions how to analyse or interpret observations from the McMaster or similar quantitative parasitic diagnostic techniques, widely used for evaluating parasite eggs in faeces. The McMaster technique can easily be shown from a theoretical perspective to give variable results that inevitably arise from the random distribution of parasite eggs in a well mixed faecal sample. The Poisson processes that lead to this variability are described and illustrative examples of the potentially large confidence intervals that can arise from observed faecal eggs counts that are calculated from the observations on a McMaster slide. Attempts to modify the McMaster technique, or indeed other quantitative techniques, to ensure uniform egg counts are doomed to failure and belie ignorance of Poisson processes. A simple method to immediately identify excess variation/poor sampling from replicate counts is provided. Copyright © 2012 Elsevier B.V. All rights reserved.

Lognormal Distribution of Cellular Uptake of Radioactivity: Statistical Analysis of α-Particle Track Autoradiography

PubMed Central

Neti, Prasad V.S.V.; Howell, Roger W.

2010-01-01

Recently, the distribution of radioactivity among a population of cells labeled with 210Po was shown to be well described by a log-normal (LN) distribution function (J Nucl Med. 2006;47:1049–1058) with the aid of autoradiography. To ascertain the influence of Poisson statistics on the interpretation of the autoradiographic data, the present work reports on a detailed statistical analysis of these earlier data. Methods The measured distributions of α-particle tracks per cell were subjected to statistical tests with Poisson, LN, and Poisson-lognormal (P-LN) models. Results The LN distribution function best describes the distribution of radioactivity among cell populations exposed to 0.52 and 3.8 kBq/mL of 210Po-citrate. When cells were exposed to 67 kBq/mL, the P-LN distribution function gave a better fit; however, the underlying activity distribution remained log-normal. Conclusion The present analysis generally provides further support for the use of LN distributions to describe the cellular uptake of radioactivity. Care should be exercised when analyzing autoradiographic data on activity distributions to ensure that Poisson processes do not distort the underlying LN distribution. PMID:18483086

Log Normal Distribution of Cellular Uptake of Radioactivity: Statistical Analysis of Alpha Particle Track Autoradiography

PubMed Central

Neti, Prasad V.S.V.; Howell, Roger W.

2008-01-01

Recently, the distribution of radioactivity among a population of cells labeled with 210Po was shown to be well described by a log normal distribution function (J Nucl Med 47, 6 (2006) 1049-1058) with the aid of an autoradiographic approach. To ascertain the influence of Poisson statistics on the interpretation of the autoradiographic data, the present work reports on a detailed statistical analyses of these data. Methods The measured distributions of alpha particle tracks per cell were subjected to statistical tests with Poisson (P), log normal (LN), and Poisson – log normal (P – LN) models. Results The LN distribution function best describes the distribution of radioactivity among cell populations exposed to 0.52 and 3.8 kBq/mL 210Po-citrate. When cells were exposed to 67 kBq/mL, the P – LN distribution function gave a better fit, however, the underlying activity distribution remained log normal. Conclusions The present analysis generally provides further support for the use of LN distributions to describe the cellular uptake of radioactivity. Care should be exercised when analyzing autoradiographic data on activity distributions to ensure that Poisson processes do not distort the underlying LN distribution. PMID:16741316

Blind beam-hardening correction from Poisson measurements

NASA Astrophysics Data System (ADS)

Gu, Renliang; Dogandžić, Aleksandar

2016-02-01

We develop a sparse image reconstruction method for Poisson-distributed polychromatic X-ray computed tomography (CT) measurements under the blind scenario where the material of the inspected object and the incident energy spectrum are unknown. We employ our mass-attenuation spectrum parameterization of the noiseless measurements and express the mass- attenuation spectrum as a linear combination of B-spline basis functions of order one. A block coordinate-descent algorithm is developed for constrained minimization of a penalized Poisson negative log-likelihood (NLL) cost function, where constraints and penalty terms ensure nonnegativity of the spline coefficients and nonnegativity and sparsity of the density map image; the image sparsity is imposed using a convex total-variation (TV) norm penalty term. This algorithm alternates between a Nesterov's proximal-gradient (NPG) step for estimating the density map image and a limited-memory Broyden-Fletcher-Goldfarb-Shanno with box constraints (L-BFGS-B) step for estimating the incident-spectrum parameters. To accelerate convergence of the density- map NPG steps, we apply function restart and a step-size selection scheme that accounts for varying local Lipschitz constants of the Poisson NLL. Real X-ray CT reconstruction examples demonstrate the performance of the proposed scheme.

Green's function enriched Poisson solver for electrostatics in many-particle systems

NASA Astrophysics Data System (ADS)

Sutmann, Godehard

2016-06-01

A highly accurate method is presented for the construction of the charge density for the solution of the Poisson equation in particle simulations. The method is based on an operator adjusted source term which can be shown to produce exact results up to numerical precision in the case of a large support of the charge distribution, therefore compensating the discretization error of finite difference schemes. This is achieved by balancing an exact representation of the known Green's function of regularized electrostatic problem with a discretized representation of the Laplace operator. It is shown that the exact calculation of the potential is possible independent of the order of the finite difference scheme but the computational efficiency for higher order methods is found to be superior due to a faster convergence to the exact result as a function of the charge support.

A spatial scan statistic for compound Poisson data.

PubMed

Rosychuk, Rhonda J; Chang, Hsing-Ming

2013-12-20

The topic of spatial cluster detection gained attention in statistics during the late 1980s and early 1990s. Effort has been devoted to the development of methods for detecting spatial clustering of cases and events in the biological sciences, astronomy and epidemiology. More recently, research has examined detecting clusters of correlated count data associated with health conditions of individuals. Such a method allows researchers to examine spatial relationships of disease-related events rather than just incident or prevalent cases. We introduce a spatial scan test that identifies clusters of events in a study region. Because an individual case may have multiple (repeated) events, we base the test on a compound Poisson model. We illustrate our method for cluster detection on emergency department visits, where individuals may make multiple disease-related visits. Copyright © 2013 John Wiley & Sons, Ltd.

A Poisson approach to the validation of failure time surrogate endpoints in individual patient data meta-analyses.

PubMed

Rotolo, Federico; Paoletti, Xavier; Burzykowski, Tomasz; Buyse, Marc; Michiels, Stefan

2017-01-01

Surrogate endpoints are often used in clinical trials instead of well-established hard endpoints for practical convenience. The meta-analytic approach relies on two measures of surrogacy: one at the individual level and one at the trial level. In the survival data setting, a two-step model based on copulas is commonly used. We present a new approach which employs a bivariate survival model with an individual random effect shared between the two endpoints and correlated treatment-by-trial interactions. We fit this model using auxiliary mixed Poisson models. We study via simulations the operating characteristics of this mixed Poisson approach as compared to the two-step copula approach. We illustrate the application of the methods on two individual patient data meta-analyses in gastric cancer, in the advanced setting (4069 patients from 20 randomized trials) and in the adjuvant setting (3288 patients from 14 randomized trials).

PB-AM: An open-source, fully analytical linear poisson-boltzmann solver.

PubMed

Felberg, Lisa E; Brookes, David H; Yap, Eng-Hui; Jurrus, Elizabeth; Baker, Nathan A; Head-Gordon, Teresa

2017-06-05

We present the open source distributed software package Poisson-Boltzmann Analytical Method (PB-AM), a fully analytical solution to the linearized PB equation, for molecules represented as non-overlapping spherical cavities. The PB-AM software package includes the generation of outputs files appropriate for visualization using visual molecular dynamics, 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-Boltzmann 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. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Relative age effect in elite soccer: More early-born players, but no better valued, and no paragon clubs or countries

PubMed Central

Doyle, John R.

2018-01-01

The paper analyses two datasets of elite soccer players (top 1000 professionals and UEFA Under-19 Youth League). In both, we find a Relative Age Effect (RAE) for frequency, but not for value. That is, while there are more players born at the start of the competition year, their transfer values are no higher, nor are they given more game time. We use Poisson regression to derive a transparent index of the discrimination present in RAE. Also, because Poisson is valid for small frequency counts, it supports analysis at the disaggregated levels of country and club. From this, we conclude there are no paragon clubs or countries immune to RAE; that is clubs and countries do not differ systematically in the RAE they experience; also, that Poisson regression is a powerful and flexible method of analysing RAE data. PMID:29420576

Study on reservoir time-varying design flood of inflow based on Poisson process with time-dependent parameters

NASA Astrophysics Data System (ADS)

Li, Jiqing; Huang, Jing; Li, Jianchang

2018-06-01

The time-varying design flood can make full use of the measured data, which can provide the reservoir with the basis of both flood control and operation scheduling. This paper adopts peak over threshold method for flood sampling in unit periods and Poisson process with time-dependent parameters model for simulation of reservoirs time-varying design flood. Considering the relationship between the model parameters and hypothesis, this paper presents the over-threshold intensity, the fitting degree of Poisson distribution and the design flood parameters are the time-varying design flood unit period and threshold discriminant basis, deduced Longyangxia reservoir time-varying design flood process at 9 kinds of design frequencies. The time-varying design flood of inflow is closer to the reservoir actual inflow conditions, which can be used to adjust the operating water level in flood season and make plans for resource utilization of flood in the basin.

Detecting isotopic ratio outliers

NASA Astrophysics Data System (ADS)

Bayne, C. K.; Smith, D. H.

An alternative method is proposed for improving isotopic ratio estimates. This method mathematically models pulse-count data and uses iterative reweighted Poisson regression to estimate model parameters to calculate the isotopic ratios. This computer-oriented approach provides theoretically better methods than conventional techniques to establish error limits and to identify outliers.

FIND: difFerential chromatin INteractions Detection using a spatial Poisson process

PubMed Central

Chen, Yang; Zhang, Michael Q.

2018-01-01

Polymer-based simulations and experimental studies indicate the existence of a spatial dependency between the adjacent DNA fibers involved in the formation of chromatin loops. However, the existing strategies for detecting differential chromatin interactions assume that the interacting segments are spatially independent from the other segments nearby. To resolve this issue, we developed a new computational method, FIND, which considers the local spatial dependency between interacting loci. FIND uses a spatial Poisson process to detect differential chromatin interactions that show a significant difference in their interaction frequency and the interaction frequency of their neighbors. Simulation and biological data analysis show that FIND outperforms the widely used count-based methods and has a better signal-to-noise ratio. PMID:29440282

Zero-truncated panel Poisson mixture models: Estimating the impact on tourism benefits in Fukushima Prefecture.

PubMed

Narukawa, Masaki; Nohara, Katsuhito

2018-04-01

This study proposes an estimation approach to panel count data, truncated at zero, in order to apply a contingent behavior travel cost method to revealed and stated preference data collected via a web-based survey. We develop zero-truncated panel Poisson mixture models by focusing on respondents who visited a site. In addition, we introduce an inverse Gaussian distribution to unobserved individual heterogeneity as an alternative to a popular gamma distribution, making it possible to capture effectively the long tail typically observed in trip data. We apply the proposed method to estimate the impact on tourism benefits in Fukushima Prefecture as a result of the Fukushima Nuclear Power Plant No. 1 accident. Copyright © 2018 Elsevier Ltd. All rights reserved.

A computer program to generate two-dimensional grids about airfoils and other shapes by the use of Poisson's equation

NASA Technical Reports Server (NTRS)

Sorenson, R. L.

1980-01-01

A method for generating two dimensional finite difference grids about airfoils and other shapes by the use of the Poisson differential equation is developed. The inhomogeneous terms are automatically chosen such that two important effects are imposed on the grid at both the inner and outer boundaries. The first effect is control of the spacing between mesh points along mesh lines intersecting the boundaries. The second effect is control of the angles with which mesh lines intersect the boundaries. A FORTRAN computer program has been written to use this method. A description of the program, a discussion of the control parameters, and a set of sample cases are included.

On the Singularity of the Vlasov-Poisson System

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

and Hong Qin, Jian Zheng

2013-04-26

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

On the singularity of the Vlasov-Poisson system

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

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

2013-09-15

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

Optimizing electrostatic field calculations with the Adaptive Poisson-Boltzmann Solver to predict electric fields at protein-protein interfaces II: explicit near-probe and hydrogen-bonding water molecules.

PubMed

Ritchie, Andrew W; Webb, Lauren J

2014-07-17

We have examined the effects of including explicit, near-probe solvent molecules in a continuum electrostatics strategy using the linear Poisson-Boltzmann equation with the Adaptive Poisson-Boltzmann Solver (APBS) to calculate electric fields at the midpoint of a nitrile bond both at the surface of a monomeric protein and when docked at a protein-protein interface. Results were compared to experimental vibrational absorption energy measurements of the nitrile oscillator. We examined three methods for selecting explicit water molecules: (1) all water molecules within 5 Å of the nitrile nitrogen; (2) the water molecule closest to the nitrile nitrogen; and (3) any single water molecule hydrogen-bonding to the nitrile. The correlation between absolute field strengths with experimental absorption energies were calculated and it was observed that method 1 was only an improvement for the monomer calculations, while methods 2 and 3 were not significantly different from the purely implicit solvent calculations for all protein systems examined. Upon taking the difference in calculated electrostatic fields and comparing to the difference in absorption frequencies, we typically observed an increase in experimental correlation for all methods, with method 1 showing the largest gain, likely due to the improved absolute monomer correlations using that method. These results suggest that, unlike with quantum mechanical methods, when calculating absolute fields using entirely classical models, implicit solvent is typically sufficient and additional work to identify hydrogen-bonding or nearest waters does not significantly impact the results. Although we observed that a sphere of solvent near the field of interest improved results for relative field calculations, it should not be consider a panacea for all situations.

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

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

Garrett, C. Kristopher; Hauck, Cory D.

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

Mixed-Poisson Point Process with Partially-Observed Covariates: Ecological Momentary Assessment of Smoking.

PubMed

Neustifter, Benjamin; Rathbun, Stephen L; Shiffman, Saul

2012-01-01

Ecological Momentary Assessment is an emerging method of data collection in behavioral research that may be used to capture the times of repeated behavioral events on electronic devices, and information on subjects' psychological states through the electronic administration of questionnaires at times selected from a probability-based design as well as the event times. A method for fitting a mixed Poisson point process model is proposed for the impact of partially-observed, time-varying covariates on the timing of repeated behavioral events. A random frailty is included in the point-process intensity to describe variation among subjects in baseline rates of event occurrence. Covariate coefficients are estimated using estimating equations constructed by replacing the integrated intensity in the Poisson score equations with a design-unbiased estimator. An estimator is also proposed for the variance of the random frailties. Our estimators are robust in the sense that no model assumptions are made regarding the distribution of the time-varying covariates or the distribution of the random effects. However, subject effects are estimated under gamma frailties using an approximate hierarchical likelihood. The proposed approach is illustrated using smoking data.

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

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

Meng, Da; Zheng, Bin; Lin, Guang

2014-08-29

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

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

DOE PAGES

Garrett, C. Kristopher; Hauck, Cory D.

2018-04-05

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

A nonlinear mechanics model of bio-inspired hierarchical lattice materials consisting of horseshoe microstructures

PubMed Central

Ma, Qiang; Cheng, Huanyu; Jang, Kyung-In; Luan, Haiwen; Hwang, Keh-Chih; Rogers, John A.; Huang, Yonggang; Zhang, Yihui

2016-01-01

Development of advanced synthetic materials that can mimic the mechanical properties of non-mineralized soft biological materials has important implications in a wide range of technologies. Hierarchical lattice materials constructed with horseshoe microstructures belong to this class of bio-inspired synthetic materials, where the mechanical responses can be tailored to match the nonlinear J-shaped stress-strain curves of human skins. The underlying relations between the J-shaped stress-strain curves and their microstructure geometry are essential in designing such systems for targeted applications. Here, a theoretical model of this type of hierarchical lattice material is developed by combining a finite deformation constitutive relation of the building block (i.e., horseshoe microstructure), with the analyses of equilibrium and deformation compatibility in the periodical lattices. The nonlinear J-shaped stress-strain curves and Poisson ratios predicted by this model agree very well with results of finite element analyses (FEA) and experiment. Based on this model, analytic solutions were obtained for some key mechanical quantities, e.g., elastic modulus, Poisson ratio, peak modulus, and critical strain around which the tangent modulus increases rapidly. A negative Poisson effect is revealed in the hierarchical lattice with triangular topology, as opposed to a positive Poisson effect in hierarchical lattices with Kagome and honeycomb topologies. The lattice topology is also found to have a strong influence on the stress-strain curve. For the three isotropic lattice topologies (triangular, Kagome and honeycomb), the hierarchical triangular lattice material renders the sharpest transition in the stress-strain curve and relative high stretchability, given the same porosity and arc angle of horseshoe microstructure. Furthermore, a demonstrative example illustrates the utility of the developed model in the rapid optimization of hierarchical lattice materials for reproducing the desired stress-strain curves of human skins. This study provides theoretical guidelines for future designs of soft bio-mimetic materials with hierarchical lattice constructions. PMID:27087704

A nonlinear mechanics model of bio-inspired hierarchical lattice materials consisting of horseshoe microstructures

NASA Astrophysics Data System (ADS)

Ma, Qiang; Cheng, Huanyu; Jang, Kyung-In; Luan, Haiwen; Hwang, Keh-Chih; Rogers, John A.; Huang, Yonggang; Zhang, Yihui

2016-05-01

Development of advanced synthetic materials that can mimic the mechanical properties of non-mineralized soft biological materials has important implications in a wide range of technologies. Hierarchical lattice materials constructed with horseshoe microstructures belong to this class of bio-inspired synthetic materials, where the mechanical responses can be tailored to match the nonlinear J-shaped stress-strain curves of human skins. The underlying relations between the J-shaped stress-strain curves and their microstructure geometry are essential in designing such systems for targeted applications. Here, a theoretical model of this type of hierarchical lattice material is developed by combining a finite deformation constitutive relation of the building block (i.e., horseshoe microstructure), with the analyses of equilibrium and deformation compatibility in the periodical lattices. The nonlinear J-shaped stress-strain curves and Poisson ratios predicted by this model agree very well with results of finite element analyses (FEA) and experiment. Based on this model, analytic solutions were obtained for some key mechanical quantities, e.g., elastic modulus, Poisson ratio, peak modulus, and critical strain around which the tangent modulus increases rapidly. A negative Poisson effect is revealed in the hierarchical lattice with triangular topology, as opposed to a positive Poisson effect in hierarchical lattices with Kagome and honeycomb topologies. The lattice topology is also found to have a strong influence on the stress-strain curve. For the three isotropic lattice topologies (triangular, Kagome and honeycomb), the hierarchical triangular lattice material renders the sharpest transition in the stress-strain curve and relative high stretchability, given the same porosity and arc angle of horseshoe microstructure. Furthermore, a demonstrative example illustrates the utility of the developed model in the rapid optimization of hierarchical lattice materials for reproducing the desired stress-strain curves of human skins. This study provides theoretical guidelines for future designs of soft bio-mimetic materials with hierarchical lattice constructions.

A nonlinear mechanics model of bio-inspired hierarchical lattice materials consisting of horseshoe microstructures.

PubMed

Ma, Qiang; Cheng, Huanyu; Jang, Kyung-In; Luan, Haiwen; Hwang, Keh-Chih; Rogers, John A; Huang, Yonggang; Zhang, Yihui

2016-05-01

Development of advanced synthetic materials that can mimic the mechanical properties of non-mineralized soft biological materials has important implications in a wide range of technologies. Hierarchical lattice materials constructed with horseshoe microstructures belong to this class of bio-inspired synthetic materials, where the mechanical responses can be tailored to match the nonlinear J-shaped stress-strain curves of human skins. The underlying relations between the J-shaped stress-strain curves and their microstructure geometry are essential in designing such systems for targeted applications. Here, a theoretical model of this type of hierarchical lattice material is developed by combining a finite deformation constitutive relation of the building block (i.e., horseshoe microstructure), with the analyses of equilibrium and deformation compatibility in the periodical lattices. The nonlinear J-shaped stress-strain curves and Poisson ratios predicted by this model agree very well with results of finite element analyses (FEA) and experiment. Based on this model, analytic solutions were obtained for some key mechanical quantities, e.g., elastic modulus, Poisson ratio, peak modulus, and critical strain around which the tangent modulus increases rapidly. A negative Poisson effect is revealed in the hierarchical lattice with triangular topology, as opposed to a positive Poisson effect in hierarchical lattices with Kagome and honeycomb topologies. The lattice topology is also found to have a strong influence on the stress-strain curve. For the three isotropic lattice topologies (triangular, Kagome and honeycomb), the hierarchical triangular lattice material renders the sharpest transition in the stress-strain curve and relative high stretchability, given the same porosity and arc angle of horseshoe microstructure. Furthermore, a demonstrative example illustrates the utility of the developed model in the rapid optimization of hierarchical lattice materials for reproducing the desired stress-strain curves of human skins. This study provides theoretical guidelines for future designs of soft bio-mimetic materials with hierarchical lattice constructions.

Analysis strategies for longitudinal attachment loss data.

PubMed

Beck, J D; Elter, J R

2000-02-01

The purpose of this invited review is to describe and discuss methods currently in use to quantify the progression of attachment loss in epidemiological studies of periodontal disease, and to make recommendations for specific analytic methods based upon the particular design of the study and structure of the data. The review concentrates on the definition of incident attachment loss (ALOSS) and its component parts; measurement issues including thresholds and regression to the mean; methods of accounting for longitudinal change, including changes in means, changes in proportions of affected sites, incidence density, the effect of tooth loss and reversals, and repeated events; statistical models of longitudinal change, including the incorporation of the time element, use of linear, logistic or Poisson regression or survival analysis, and statistical tests; site vs person level of analysis, including statistical adjustment for correlated data; the strengths and limitations of ALOSS data. Examples from the Piedmont 65+ Dental Study are used to illustrate specific concepts. We conclude that incidence density is the preferred methodology to use for periodontal studies with more than one period of follow-up and that the use of studies not employing methods for dealing with complex samples, correlated data, and repeated measures does not take advantage of our current understanding of the site- and person-level variables important in periodontal disease and may generate biased results.

Spatial event cluster detection using an approximate normal distribution.

PubMed

Torabi, Mahmoud; Rosychuk, Rhonda J

2008-12-12

In geographic surveillance of disease, areas with large numbers of disease cases are to be identified so that investigations of the causes of high disease rates can be pursued. Areas with high rates are called disease clusters and statistical cluster detection tests are used to identify geographic areas with higher disease rates than expected by chance alone. Typically cluster detection tests are applied to incident or prevalent cases of disease, but surveillance of disease-related events, where an individual may have multiple events, may also be of interest. Previously, a compound Poisson approach that detects clusters of events by testing individual areas that may be combined with their neighbours has been proposed. However, the relevant probabilities from the compound Poisson distribution are obtained from a recursion relation that can be cumbersome if the number of events are large or analyses by strata are performed. We propose a simpler approach that uses an approximate normal distribution. This method is very easy to implement and is applicable to situations where the population sizes are large and the population distribution by important strata may differ by area. We demonstrate the approach on pediatric self-inflicted injury presentations to emergency departments and compare the results for probabilities based on the recursion and the normal approach. We also implement a Monte Carlo simulation to study the performance of the proposed approach. In a self-inflicted injury data example, the normal approach identifies twelve out of thirteen of the same clusters as the compound Poisson approach, noting that the compound Poisson method detects twelve significant clusters in total. Through simulation studies, the normal approach well approximates the compound Poisson approach for a variety of different population sizes and case and event thresholds. A drawback of the compound Poisson approach is that the relevant probabilities must be determined through a recursion relation and such calculations can be computationally intensive if the cluster size is relatively large or if analyses are conducted with strata variables. On the other hand, the normal approach is very flexible, easily implemented, and hence, more appealing for users. Moreover, the concepts may be more easily conveyed to non-statisticians interested in understanding the methodology associated with cluster detection test results.

Nambu-Poisson gauge theory

NASA Astrophysics Data System (ADS)

Jurčo, Branislav; Schupp, Peter; Vysoký, Jan

2014-06-01

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

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.

Analysis of tablet compaction. I. Characterization of mechanical behavior of powder and powder/tooling friction.

PubMed

Cunningham, J C; Sinka, I C; Zavaliangos, A

2004-08-01

In this first of two articles on the modeling of tablet compaction, the experimental inputs related to the constitutive model of the powder and the powder/tooling friction are determined. The continuum-based analysis of tableting makes use of an elasto-plastic model, which incorporates the elements of yield, plastic flow potential, and hardening, to describe the mechanical behavior of microcrystalline cellulose over the range of densities experienced during tableting. Specifically, a modified Drucker-Prager/cap plasticity model, which includes material parameters such as cohesion, internal friction, and hydrostatic yield pressure that evolve with the internal state variable relative density, was applied. Linear elasticity is assumed with the elastic parameters, Young's modulus, and Poisson's ratio dependent on the relative density. The calibration techniques were developed based on a series of simple mechanical tests including diametrical compression, simple compression, and die compaction using an instrumented die. The friction behavior is measured using an instrumented die and the experimental data are analyzed using the method of differential slices. The constitutive model and frictional properties are essential experimental inputs to the finite element-based model described in the companion article. Copyright 2004 Wiley-Liss, Inc. and the American Pharmacists Association J Pharm Sci 93:2022-2039, 2004

Mass and charge transport in IPMC actuators with fractal interfaces

NASA Astrophysics Data System (ADS)

Chang, Longfei; Wu, Yucheng; Zhu, Zicai; Li, Heng

2016-04-01

Ionic Polymer-Metal Composite (IPMC) actuators have been attracting a growing interest in extensive applications, which consequently raises the demands on the accuracy of its theoretical modeling. For the last few years, rough landscape of the interface between the electrode and the ionic membrane of IPMC has been well-documented as one of the key elements to ensure a satisfied performance. However, in most of the available work, the interface morphology of IPMC was simplified with structural idealization, which lead to perplexity in the physical interpretation on its interface mechanism. In this paper, the quasi-random rough interface of IPMC was described with fractal dimension and scaling parameters. And the electro-chemical field was modeled by Poisson equation and a properly simplified Nernst-Planck equation set. Then, by simulation with Finite Element Method, a comprehensive analysis on he inner mass and charge transportation in IPMC actuators with different fractal interfaces was provided, which may be further adopted to instruct the performance-oriented interface design for ionic electro-active actuators. The results also verified that rough interface can impact the electrical and mechanical response of IPMC, not only from the respect of the real surface increase, but also from mass distribution difference caused by the complexity of the micro profile.

Single-step scanner-based digital image correlation (SB-DIC) method for large deformation mapping in rubber

NASA Astrophysics Data System (ADS)

Goh, C. P.; Ismail, H.; Yen, K. S.; Ratnam, M. M.

2017-01-01

The incremental digital image correlation (DIC) method has been applied in the past to determine strain in large deformation materials like rubber. This method is, however, prone to cumulative errors since the total displacement is determined by combining the displacements in numerous stages of the deformation. In this work, a method of mapping large strains in rubber using DIC in a single-step without the need for a series of deformation images is proposed. The reference subsets were deformed using deformation factors obtained from the fitted mean stress-axial stretch ratio curve obtained experimentally and the theoretical Poisson function. The deformed reference subsets were then correlated with the deformed image after loading. The recently developed scanner-based digital image correlation (SB-DIC) method was applied on dumbbell rubber specimens to obtain the in-plane displacement fields up to 350% axial strain. Comparison of the mean axial strains determined from the single-step SB-DIC method with those from the incremental SB-DIC method showed an average difference of 4.7%. Two rectangular rubber specimens containing circular and square holes were deformed and analysed using the proposed method. The resultant strain maps from the single-step SB-DIC method were compared with the results of finite element modeling (FEM). The comparison shows that the proposed single-step SB-DIC method can be used to map the strain distribution accurately in large deformation materials like rubber at much shorter time compared to the incremental DIC method.

Tenth NASTRAN User's Colloquium

NASA Technical Reports Server (NTRS)

1982-01-01

The development of the NASTRAN computer program, a general purpose finite element computer code for structural analysis, was discussed. The application and development of NASTRAN is presented in the following topics: improvements and enhancements; developments of pre and postprocessors; interactive review system; the use of harmonic expansions in magnetic field problems; improving a dynamic model with test data using Linwood; solution of axisymmetric fluid structure interaction problems; large displacements and stability analysis of nonlinear propeller structures; prediction of bead area contact load at the tire wheel interface; elastic plastic analysis of an overloaded breech ring; finite element solution of torsion and other 2-D Poisson equations; new capability for elastic aircraft airloads; usage of substructuring analysis in the get away special program; solving symmetric structures with nonsymmetric loads; evaluation and reduction of errors induced by Guyan transformation.

Microstructure-based hyperelastic models for closed-cell solids.

PubMed

Mihai, L Angela; Wyatt, Hayley; Goriely, Alain

2017-04-01

For cellular bodies involving large elastic deformations, mesoscopic continuum models that take into account the interplay between the geometry and the microstructural responses of the constituents are developed, analysed and compared with finite-element simulations of cellular structures with different architecture. For these models, constitutive restrictions for the physical plausibility of the material responses are established, and global descriptors such as nonlinear elastic and shear moduli and Poisson's ratio are obtained from the material characteristics of the constituents. Numerical results show that these models capture well the mechanical responses of finite-element simulations for three-dimensional periodic structures of neo-Hookean material with closed cells under large tension. In particular, the mesoscopic models predict the macroscopic stiffening of the structure when the stiffness of the cell-core increases.

Microstructure-based hyperelastic models for closed-cell solids

NASA Astrophysics Data System (ADS)

Mihai, L. Angela; Wyatt, Hayley; Goriely, Alain

2017-04-01

For cellular bodies involving large elastic deformations, mesoscopic continuum models that take into account the interplay between the geometry and the microstructural responses of the constituents are developed, analysed and compared with finite-element simulations of cellular structures with different architecture. For these models, constitutive restrictions for the physical plausibility of the material responses are established, and global descriptors such as nonlinear elastic and shear moduli and Poisson's ratio are obtained from the material characteristics of the constituents. Numerical results show that these models capture well the mechanical responses of finite-element simulations for three-dimensional periodic structures of neo-Hookean material with closed cells under large tension. In particular, the mesoscopic models predict the macroscopic stiffening of the structure when the stiffness of the cell-core increases.

Fiber shape effects on metal matrix composite behavior

NASA Technical Reports Server (NTRS)

Brown, H. C.; Lee, H.-J.; Chamis, C. C.

1992-01-01

The effects of different fiber shapes on the behavior of a SiC/Ti-15 metal matrix composite is computationally simulated. A three-dimensional finite element model consisting of a group of nine unidirectional fibers is used in the analysis. The model is employed to represent five different fiber shapes: a circle, an ellipse, a kidney, and two different cross shapes. The distribution of microstresses and the composite material properties, such as moduli, coefficients of thermal expansion, and Poisson's ratios, are obtained from the finite element analysis for the various fiber shapes. Comparisons of these results are used to determine the sensitivity of the composite behavior to the different fiber shapes and assess their potential benefits. No clear benefits result from different fiber shapes though there are some increases/decreases in isolated properties.

Numerical calculations of velocity and pressure distribution around oscillating airfoils

NASA Technical Reports Server (NTRS)

Bratanow, T.; Ecer, A.; Kobiske, M.

1974-01-01

An analytical procedure based on the Navier-Stokes equations was developed for analyzing and representing properties of unsteady viscous flow around oscillating obstacles. A variational formulation of the vorticity transport equation was discretized in finite element form and integrated numerically. At each time step of the numerical integration, the velocity field around the obstacle was determined for the instantaneous vorticity distribution from the finite element solution of Poisson's equation. The time-dependent boundary conditions around the oscillating obstacle were introduced as external constraints, using the Lagrangian Multiplier Technique, at each time step of the numerical integration. The procedure was then applied for determining pressures around obstacles oscillating in unsteady flow. The obtained results for a cylinder and an airfoil were illustrated in the form of streamlines and vorticity and pressure distributions.

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.

From Loss of Memory to Poisson.

ERIC Educational Resources Information Center

Johnson, Bruce R.

1983-01-01

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

Towards an acoustic model-based poroelastic imaging method: I. Theoretical foundation.

PubMed

Berry, Gearóid P; Bamber, Jeffrey C; Armstrong, Cecil G; Miller, Naomi R; Barbone, Paul E

2006-04-01

The ultrasonic measurement and imaging of tissue elasticity is currently under wide investigation and development as a clinical tool for the assessment of a broad range of diseases, but little account in this field has yet been taken of the fact that soft tissue is porous and contains mobile fluid. The ability to squeeze fluid out of tissue may have implications for conventional elasticity imaging, and may present opportunities for new investigative tools. When a homogeneous, isotropic, fluid-saturated poroelastic material with a linearly elastic solid phase and incompressible solid and fluid constituents is subjected to stress, the behaviour of the induced internal strain field is influenced by three material constants: the Young's modulus (E(s)) and Poisson's ratio (nu(s)) of the solid matrix and the permeability (k) of the solid matrix to the pore fluid. New analytical expressions were derived and used to model the time-dependent behaviour of the strain field inside simulated homogeneous cylindrical samples of such a poroelastic material undergoing sustained unconfined compression. A model-based reconstruction technique was developed to produce images of parameters related to the poroelastic material constants (E(s), nu(s), k) from a comparison of the measured and predicted time-dependent spatially varying radial strain. Tests of the method using simulated noisy strain data showed that it is capable of producing three unique parametric images: an image of the Poisson's ratio of the solid matrix, an image of the axial strain (which was not time-dependent subsequent to the application of the compression) and an image representing the product of the aggregate modulus E(s)(1-nu(s))/(1+nu(s))(1-2nu(s)) of the solid matrix and the permeability of the solid matrix to the pore fluid. The analytical expressions were further used to numerically validate a finite element model and to clarify previous work on poroelastography.

Calculated and measured fields in superferric wiggler magnets

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

Blum, E.B.; Solomon, L.

1995-02-01

Although Klaus Halbach is widely known and appreciated as the originator of the computer program POISSON for electromagnetic field calculation, Klaus has always believed that analytical methods can give much more insight into the performance of a magnet than numerical simulation. Analytical approximations readily show how the different aspects of a magnet`s design such as pole dimensions, current, and coil configuration contribute to the performance. These methods yield accuracies of better than 10%. Analytical methods should therefore be used when conceptualizing a magnet design. Computer analysis can then be used for refinement. A simple model is presented for the peakmore » on-axis field of an electro-magnetic wiggler with iron poles and superconducting coils. The model is applied to the radiator section of the superconducting wiggler for the BNL Harmonic Generation Free Electron Laser. The predictions of the model are compared to the measured field and the results from POISSON.« less

Method selection and adaptation for distributed monitoring of infectious diseases for syndromic surveillance.

PubMed

Xing, Jian; Burkom, Howard; Tokars, Jerome

2011-12-01

Automated surveillance systems require statistical methods to recognize increases in visit counts that might indicate an outbreak. In prior work we presented methods to enhance the sensitivity of C2, a commonly used time series method. In this study, we compared the enhanced C2 method with five regression models. We used emergency department chief complaint data from US CDC BioSense surveillance system, aggregated by city (total of 206 hospitals, 16 cities) during 5/2008-4/2009. Data for six syndromes (asthma, gastrointestinal, nausea and vomiting, rash, respiratory, and influenza-like illness) was used and was stratified by mean count (1-19, 20-49, ≥50 per day) into 14 syndrome-count categories. We compared the sensitivity for detecting single-day artificially-added increases in syndrome counts. Four modifications of the C2 time series method, and five regression models (two linear and three Poisson), were tested. A constant alert rate of 1% was used for all methods. Among the regression models tested, we found that a Poisson model controlling for the logarithm of total visits (i.e., visits both meeting and not meeting a syndrome definition), day of week, and 14-day time period was best. Among 14 syndrome-count categories, time series and regression methods produced approximately the same sensitivity (<5% difference) in 6; in six categories, the regression method had higher sensitivity (range 6-14% improvement), and in two categories the time series method had higher sensitivity. When automated data are aggregated to the city level, a Poisson regression model that controls for total visits produces the best overall sensitivity for detecting artificially added visit counts. This improvement was achieved without increasing the alert rate, which was held constant at 1% for all methods. These findings will improve our ability to detect outbreaks in automated surveillance system data. Published by Elsevier Inc.

Characterization and modelling of magneto-auxeticity, the magnetically induced auxetic behavior, in Galfenol

NASA Astrophysics Data System (ADS)

Raghunath, Ganesh

Iron-Gallium alloy (Galfenol) is a magnetostrictive smart material (lambdasat ˜400 ppm) with potential for robust transduction owing to good magneto-mechanical coupling and useful mechanical properties. In addition, Galfenol exhibits a highly negative Poisson's ratio (denoted by nu) along the crystallographic directions on {100} planes with nu values of as low as -0.7 under tensile loads. Consequently, their samples become wider when elongated and narrower when compressed (aka auxeticity). This is an anisotropic, in-plane and volume conserving phenomenon with compensating contractions and expansions in the third (out of plane) direction. Since there is good magneto-elastic coupling in Galfenol, a negative Poisson's ratio is expected to be observed under application of magnetic fields even under zero stress conditions. This work deals with systematically studying the magneto-elastic contributions in Galfenol samples between 12 and 33 atomic percent Ga as a non-synthetic (no artificial linkages, unlike foams) 'structural auxetic' material, capable of bearing loads. This investigation addresses the profound gap in understanding this atypical behavior using empirical data supported by analytical modeling from first principles to predict the Poisson's ratio at magnetic saturation, multi-physics finite element simulations to determine the trends in the strains along the {100} directions and magnetic domain imaging to explain the mechanical response from a magnetic domain perspective. The outcome of this effort will help comprehend the association between anisotropic magnetic and mechanical energies and hence the magnetic contributions to the atomic level interactions that are the origins of this magneto-auxetic characteristic. Also, it is well established that a number of mechanical properties such as shear resistance and toughness depend on the value of Poisson's ratio. There is a slight increase in these mechanical properties with non-zero nu values, but as we enter the highly auxetic regime (nu<-0.5), these values increase by magnitudes. Hence, the possibility of nu values approaching -1.0 under applied magnetic fields at zero stress is extremely intriguing, as these properties can be much larger than is possible in conventional materials. This has potential for several novel applications where the value of Poisson's ratio can be magnetically tuned to keep it near -1 under applied stresses.

Poisson Noise Removal in Spherical Multichannel Images: Application to Fermi data

NASA Astrophysics Data System (ADS)

Schmitt, Jérémy; Starck, Jean-Luc; Fadili, Jalal; Digel, Seth

2012-03-01

The Fermi Gamma-ray Space Telescope, which was launched by NASA in June 2008, is a powerful space observatory which studies the high-energy gamma-ray sky [5]. Fermi's main instrument, the Large Area Telescope (LAT), detects photons in an energy range between 20MeV and >300 GeV. The LAT is much more sensitive than its predecessor, the energetic gamma ray experiment telescope (EGRET) telescope on the Compton Gamma-ray Observatory, and is expected to find several thousand gamma-ray point sources, which is an order of magnitude more than its predecessor EGRET [13]. Even with its relatively large acceptance (∼2m2 sr), the number of photons detected by the LAT outside the Galactic plane and away from intense sources is relatively low and the sky overall has a diffuse glow from cosmic-ray interactions with interstellar gas and low energy photons that makes a background against which point sources need to be detected. In addition, the per-photon angular resolution of the LAT is relatively poor and strongly energy dependent, ranging from>10° at 20MeV to ∼0.1° above 100 GeV. Consequently, the spherical photon count images obtained by Fermi are degraded by the fluctuations on the number of detected photons. This kind of noise is strongly signal dependent : on the brightest parts of the image like the galactic plane or the brightest sources, we have a lot of photons per pixel, and so the photon noise is low. Outside the galactic plane, the number of photons per pixel is low, which means that the photon noise is high. Such a signal-dependent noise cannot be accurately modeled by a Gaussian distribution. The basic photon-imaging model assumes that the number of detected photons at each pixel location is Poisson distributed. More specifically, the image is considered as a realization of an inhomogeneous Poisson process. This statistical noise makes the source detection more difficult, consequently it is highly desirable to have an efficient denoising method for spherical Poisson data. Several techniques have been proposed in the literature to estimate Poisson intensity in 2-dimensional (2D). A major class of methods adopt a multiscale Bayesian framework specifically tailored for Poisson data [18], independently initiated by Timmerman and Nowak [23] and Kolaczyk [14]. Lefkimmiaits et al. [15] proposed an improved Bayesian framework for analyzing Poisson processes, based on a multiscale representation of the Poisson process in which the ratios of the underlying Poisson intensities in adjacent scales are modeled as mixtures of conjugate parametric distributions. Another approach includes preprocessing the count data by a variance stabilizing transform(VST) such as theAnscombe [4] and the Fisz [10] transforms, applied respectively in the spatial [8] or in the wavelet domain [11]. The transform reforms the data so that the noise approximately becomes Gaussian with a constant variance. Standard techniques for independent identically distributed Gaussian noise are then used for denoising. Zhang et al. [25] proposed a powerful method called multiscale (MS-VST). It consists in combining a VST with a multiscale transform (wavelets, ridgelets, or curvelets), yielding asymptotically normally distributed coefficients with known variances. The interest of using a multiscale method is to exploit the sparsity properties of the data : the data are transformed into a domain in which it is sparse, and, as the noise is not sparse in any transform domain, it is easy to separate it from the signal. When the noise is Gaussian of known variance, it is easy to remove it with a high thresholding in the wavelet domain. The choice of the multiscale transform depends on the morphology of the data. Wavelets represent more efficiently regular structures and isotropic singularities, whereas ridgelets are designed to represent global lines in an image, and curvelets represent efficiently curvilinear contours. Significant coefficients are then detected with binary hypothesis testing, and the final estimate is reconstructed with an iterative scheme. In Ref

Performance of Nonlinear Finite-Difference Poisson-Boltzmann Solvers

PubMed Central

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

2014-01-01

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

Nonlocal Poisson-Fermi model for ionic solvent.

PubMed

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

2016-07-01

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

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.

Improvements to the APBS biomolecular solvation software suite: Improvements to the APBS Software Suite

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

Jurrus, Elizabeth; Engel, Dave; Star, Keith

The Adaptive Poisson-Boltzmann Solver (APBS) software was developed to solve the equations of continuum electrostatics for large biomolecular assemblages that has provided impact in the study of a broad range of chemical, biological, and biomedical applications. APBS addresses three key technology challenges for understanding solvation and electrostatics in biomedical applications: accurate and efficient models for biomolecular solvation and electrostatics, robust and scalable software for applying those theories to biomolecular systems, and mechanisms for sharing and analyzing biomolecular electrostatics data in the scientific community. To address new research applications and advancing computational capabilities, we have continually updated APBS and its suitemore » of accompanying software since its release in 2001. In this manuscript, we discuss the models and capabilities that have recently been implemented within the APBS software package including: a Poisson-Boltzmann analytical and a semi-analytical solver, an optimized boundary element solver, a geometry-based geometric flow solvation model, a graph theory based algorithm for determining pKa values, and an improved web-based visualization tool for viewing electrostatics.« less

Improvements to the APBS biomolecular solvation software suite.

PubMed

Jurrus, Elizabeth; Engel, Dave; Star, Keith; Monson, Kyle; Brandi, Juan; Felberg, Lisa E; Brookes, David H; Wilson, Leighton; Chen, Jiahui; Liles, Karina; Chun, Minju; Li, Peter; Gohara, David W; Dolinsky, Todd; Konecny, Robert; Koes, David R; Nielsen, Jens Erik; Head-Gordon, Teresa; Geng, Weihua; Krasny, Robert; Wei, Guo-Wei; Holst, Michael J; McCammon, J Andrew; Baker, Nathan A

2018-01-01

The Adaptive Poisson-Boltzmann Solver (APBS) software was developed to solve the equations of continuum electrostatics for large biomolecular assemblages that have provided impact in the study of a broad range of chemical, biological, and biomedical applications. APBS addresses the three key technology challenges for understanding solvation and electrostatics in biomedical applications: accurate and efficient models for biomolecular solvation and electrostatics, robust and scalable software for applying those theories to biomolecular systems, and mechanisms for sharing and analyzing biomolecular electrostatics data in the scientific community. To address new research applications and advancing computational capabilities, we have continually updated APBS and its suite of accompanying software since its release in 2001. In this article, we discuss the models and capabilities that have recently been implemented within the APBS software package including a Poisson-Boltzmann analytical and a semi-analytical solver, an optimized boundary element solver, a geometry-based geometric flow solvation model, a graph theory-based algorithm for determining pK a values, and an improved web-based visualization tool for viewing electrostatics. © 2017 The Protein Society.

Microstructure and micromechanical elastic properties of weak layers

NASA Astrophysics Data System (ADS)

Köchle, Berna; Matzl, Margret; Proksch, Martin; Schneebeli, Martin

2014-05-01

Weak layers are the mechanically most important stratigraphic layer for avalanches. Yet, there is little known about their exact geometry and their micromechanical properties. To distinguish weak layers or interfaces is essential to assess stability. However, except by destructive mechanical tests, they cannot be easily identified and characterized in the field. We casted natural weak layers and their adjacent layers in the field during two winter seasons and scanned them non-destructively with X-ray computer tomography with a resolution between 10 - 20 µm. Reconstructed three-dimensional models of centimeter-sized layered samples allow for calculating the change of structural properties. We found that structural transitions cannot always by expressed by geometry like density or grain size. In addition, we calculated the Young's modulus and Poisson's ratio of the individual layers with voxel-based finite element simulations. As any material has its characteristic elastic parameters, they may potentially differentiate individual layers, and therefore different microstructures. Our results show that Young's modulus correlates well with density but do not indicate snow's microstructure, in contrast to Poisson's ratio which tends to be lower for strongly anisotropic forms like cup crystals and facets.

A Liouville Problem for the Stationary Fractional Navier-Stokes-Poisson System

NASA Astrophysics Data System (ADS)

Wang, Y.; Xiao, J.

2017-06-01

This paper deals with a Liouville problem for the stationary fractional Navier-Stokes-Poisson system whose special case k=0 covers the compressible and incompressible time-independent fractional Navier-Stokes systems in R^{N≥2} . An essential difficulty raises from the fractional Laplacian, which is a non-local operator and thus makes the local analysis unsuitable. To overcome the difficulty, we utilize a recently-introduced extension-method in Wang and Xiao (Commun Contemp Math 18(6):1650019, 2016) which develops Caffarelli-Silvestre's technique in Caffarelli and Silvestre (Commun Partial Diff Equ 32:1245-1260, 2007).

A Liouville Problem for the Stationary Fractional Navier-Stokes-Poisson System

NASA Astrophysics Data System (ADS)

Wang, Y.; Xiao, J.

2018-06-01

This paper deals with a Liouville problem for the stationary fractional Navier-Stokes-Poisson system whose special case k=0 covers the compressible and incompressible time-independent fractional Navier-Stokes systems in R^{N≥2}. An essential difficulty raises from the fractional Laplacian, which is a non-local operator and thus makes the local analysis unsuitable. To overcome the difficulty, we utilize a recently-introduced extension-method in Wang and Xiao (Commun Contemp Math 18(6):1650019, 2016) which develops Caffarelli-Silvestre's technique in Caffarelli and Silvestre (Commun Partial Diff Equ 32:1245-1260, 2007).

FluBreaks: early epidemic detection from Google flu trends.

PubMed

Pervaiz, Fahad; Pervaiz, Mansoor; Abdur Rehman, Nabeel; Saif, Umar

2012-10-04

The Google Flu Trends service was launched in 2008 to track changes in the volume of online search queries related to flu-like symptoms. Over the last few years, the trend data produced by this service has shown a consistent relationship with the actual number of flu reports collected by the US Centers for Disease Control and Prevention (CDC), often identifying increases in flu cases weeks in advance of CDC records. However, contrary to popular belief, Google Flu Trends is not an early epidemic detection system. Instead, it is designed as a baseline indicator of the trend, or changes, in the number of disease cases. To evaluate whether these trends can be used as a basis for an early warning system for epidemics. We present the first detailed algorithmic analysis of how Google Flu Trends can be used as a basis for building a fully automated system for early warning of epidemics in advance of methods used by the CDC. Based on our work, we present a novel early epidemic detection system, called FluBreaks (dritte.org/flubreaks), based on Google Flu Trends data. We compared the accuracy and practicality of three types of algorithms: normal distribution algorithms, Poisson distribution algorithms, and negative binomial distribution algorithms. We explored the relative merits of these methods, and related our findings to changes in Internet penetration and population size for the regions in Google Flu Trends providing data. Across our performance metrics of percentage true-positives (RTP), percentage false-positives (RFP), percentage overlap (OT), and percentage early alarms (EA), Poisson- and negative binomial-based algorithms performed better in all except RFP. Poisson-based algorithms had average values of 99%, 28%, 71%, and 76% for RTP, RFP, OT, and EA, respectively, whereas negative binomial-based algorithms had average values of 97.8%, 17.8%, 60%, and 55% for RTP, RFP, OT, and EA, respectively. Moreover, the EA was also affected by the region's population size. Regions with larger populations (regions 4 and 6) had higher values of EA than region 10 (which had the smallest population) for negative binomial- and Poisson-based algorithms. The difference was 12.5% and 13.5% on average in negative binomial- and Poisson-based algorithms, respectively. We present the first detailed comparative analysis of popular early epidemic detection algorithms on Google Flu Trends data. We note that realizing this opportunity requires moving beyond the cumulative sum and historical limits method-based normal distribution approaches, traditionally employed by the CDC, to negative binomial- and Poisson-based algorithms to deal with potentially noisy search query data from regions with varying population and Internet penetrations. Based on our work, we have developed FluBreaks, an early warning system for flu epidemics using Google Flu Trends.

FIND: difFerential chromatin INteractions Detection using a spatial Poisson process.

PubMed

Djekidel, Mohamed Nadhir; Chen, Yang; Zhang, Michael Q

2018-02-12

Polymer-based simulations and experimental studies indicate the existence of a spatial dependency between the adjacent DNA fibers involved in the formation of chromatin loops. However, the existing strategies for detecting differential chromatin interactions assume that the interacting segments are spatially independent from the other segments nearby. To resolve this issue, we developed a new computational method, FIND, which considers the local spatial dependency between interacting loci. FIND uses a spatial Poisson process to detect differential chromatin interactions that show a significant difference in their interaction frequency and the interaction frequency of their neighbors. Simulation and biological data analysis show that FIND outperforms the widely used count-based methods and has a better signal-to-noise ratio. © 2018 Djekidel et al.; Published by Cold Spring Harbor Laboratory Press.

More on approximations of Poisson probabilities

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

Kao, C

1980-05-01

Calculation of Poisson probabilities frequently involves calculating high factorials, which becomes tedious and time-consuming with regular calculators. The usual way to overcome this difficulty has been to find approximations by making use of the table of the standard normal distribution. A new transformation proposed by Kao in 1978 appears to perform better for this purpose than traditional transformations. In the present paper several approximation methods are stated and compared numerically, including an approximation method that utilizes a modified version of Kao's transformation. An approximation based on a power transformation was found to outperform those based on the square-root type transformationsmore » as proposed in literature. The traditional Wilson-Hilferty approximation and Makabe-Morimura approximation are extremely poor compared with this approximation. 4 tables. (RWR)« less

Equilibrium structures of carbon diamond-like clusters and their elastic properties

NASA Astrophysics Data System (ADS)

Lisovenko, D. S.; Baimova, Yu. A.; Rysaeva, L. Kh.; Gorodtsov, V. A.; Dmitriev, S. V.

2017-04-01

Three-dimensional carbon diamond-like phases consisting of sp 3-hybridized atoms, obtained by linking of carcasses of fullerene-like molecules, are studied by methods of molecular dynamics modeling. For eight cubic and one hexagonal diamond-like phases on the basis of four types of fullerene-like molecules, equilibrium configurations are found and the elastic constants are calculated. The results obtained by the method of molecular dynamics are used for analytical calculations of the elastic characteristics of the diamond- like phases with the cubic and hexagonal anisotropy. It is found that, for a certain choice of the dilatation axis, three of these phases have negative Poisson's ratio, i.e., are partial auxetics. The variability of the engineering elasticity coefficients (Young's modulus, Poisson's ratio, shear modulus, and bulk modulus) is analyzed.

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

NASA Technical Reports Server (NTRS)

Lakes, R. S.

1992-01-01

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

Solving the problem of negative populations in approximate accelerated stochastic simulations using the representative reaction approach.

PubMed

Kadam, Shantanu; Vanka, Kumar

2013-02-15

Methods based on the stochastic formulation of chemical kinetics have the potential to accurately reproduce the dynamical behavior of various biochemical systems of interest. However, the computational expense makes them impractical for the study of real systems. Attempts to render these methods practical have led to the development of accelerated methods, where the reaction numbers are modeled by Poisson random numbers. However, for certain systems, such methods give rise to physically unrealistic negative numbers for species populations. The methods which make use of binomial variables, in place of Poisson random numbers, have since become popular, and have been partially successful in addressing this problem. In this manuscript, the development of two new computational methods, based on the representative reaction approach (RRA), has been discussed. The new methods endeavor to solve the problem of negative numbers, by making use of tools like the stochastic simulation algorithm and the binomial method, in conjunction with the RRA. It is found that these newly developed methods perform better than other binomial methods used for stochastic simulations, in resolving the problem of negative populations. Copyright © 2012 Wiley Periodicals, Inc.

Communication: Modeling charge-sign asymmetric solvation free energies with nonlinear boundary conditions

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

Bardhan, Jaydeep P.; Knepley, Matthew G.

2014-10-07

We show that charge-sign-dependent asymmetric hydration can be modeled accurately using linear Poisson theory after replacing the standard electric-displacement boundary condition with a simple nonlinear boundary condition. Using a single multiplicative scaling factor to determine atomic radii from molecular dynamics Lennard-Jones parameters, the new model accurately reproduces MD free-energy calculations of hydration asymmetries for: (i) monatomic ions, (ii) titratable amino acids in both their protonated and unprotonated states, and (iii) the Mobley “bracelet” and “rod” test problems [D. L. Mobley, A. E. Barber II, C. J. Fennell, and K. A. Dill, “Charge asymmetries in hydration of polar solutes,” J. Phys.more » Chem. B 112, 2405–2414 (2008)]. Remarkably, the model also justifies the use of linear response expressions for charging free energies. Our boundary-element method implementation demonstrates the ease with which other continuum-electrostatic solvers can be extended to include asymmetry.« less

Intrinsic delay of permeable base transistor

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

Chen, Wenchao; Guo, Jing; So, Franky

2014-07-28

Permeable base transistors (PBTs) fabricated by vacuum deposition or solution process have the advantages of easy fabrication and low power operation and are a promising device structure for flexible electronics. Intrinsic delay of PBT, which characterizes the speed of the transistor, is investigated by solving the three-dimensional Poisson equation and drift-diffusion equation self-consistently using finite element method. Decreasing the emitter thickness lowers the intrinsic delay by improving on-current, and a thinner base is also preferred for low intrinsic delay because of fewer carriers in the base region at off-state. The intrinsic delay exponentially decreases as the emitter contact Schottky barriermore » height decreases, and it linearly depends on the carrier mobility. With an optimized emitter contact barrier height and device geometry, a sub-nano-second intrinsic delay can be achieved with a carrier mobility of ∼10 cm{sup 2}/V/s obtainable in solution processed indium gallium zinc oxide, which indicates the potential of solution processed PBTs for GHz operations.« less

Laplace-SGBEM analysis of the dynamic stress intensity factors and the dynamic T-stress for the interaction between a crack and auxetic inclusions

NASA Astrophysics Data System (ADS)

Kwon, Kibum

A dynamic analysis of the interaction between a crack and an auxetic (negative Poisson ratio)/non-auxetic inclusion is presented. The two most important fracture parameters, namely the stress intensity factors and the T-stress are analyzed by using the symmetric Galerkin boundary element method in the Laplace domain for three different models of crack-inclusion interaction. To investigate the effects of auxetic inclusions on the fracture behavior of composites reinforced by this new type of material, comparisons of the dynamic stress intensity factors and the dynamic T-stress are made between the use of auxetic inclusions as opposed to the use of traditional inclusions. Furthermore, the technique presented in this research can be employed to analyze for the interaction between a crack and a cluster of auxetic/non-auxetic inclusions. Results from the latter models can be employed in crack growth analysis in auxetic-fiber-reinforced composites.

[Statistical (Poisson) motor unit number estimation. Methodological aspects and normal results in the extensor digitorum brevis muscle of healthy subjects].

PubMed

Murga Oporto, L; Menéndez-de León, C; Bauzano Poley, E; Núñez-Castaín, M J

Among the differents techniques for motor unit number estimation (MUNE) there is the statistical one (Poisson), in which the activation of motor units is carried out by electrical stimulation and the estimation performed by means of a statistical analysis based on the Poisson s distribution. The study was undertaken in order to realize an approximation to the MUNE Poisson technique showing a coprehensible view of its methodology and also to obtain normal results in the extensor digitorum brevis muscle (EDB) from a healthy population. One hundred fourteen normal volunteers with age ranging from 10 to 88 years were studied using the MUNE software contained in a Viking IV system. The normal subjects were divided into two age groups (10 59 and 60 88 years). The EDB MUNE from all them was 184 49. Both, the MUNE and the amplitude of the compound muscle action potential (CMAP) were significantly lower in the older age group (p< 0.0001), showing the MUNE a better correlation with age than CMAP amplitude ( 0.5002 and 0.4142, respectively p< 0.0001). Statistical MUNE method is an important way for the assessment to the phisiology of the motor unit. The value of MUNE correlates better with the neuromuscular aging process than CMAP amplitude does.

Bayesian semi-parametric analysis of Poisson change-point regression models: application to policy making in Cali, Colombia.

PubMed

Park, Taeyoung; Krafty, Robert T; Sánchez, Alvaro I

2012-07-27

A Poisson regression model with an offset assumes a constant baseline rate after accounting for measured covariates, which may lead to biased estimates of coefficients in an inhomogeneous Poisson process. To correctly estimate the effect of time-dependent covariates, we propose a Poisson change-point regression model with an offset that allows a time-varying baseline rate. When the nonconstant pattern of a log baseline rate is modeled with a nonparametric step function, the resulting semi-parametric model involves a model component of varying dimension and thus requires a sophisticated varying-dimensional inference to obtain correct estimates of model parameters of fixed dimension. To fit the proposed varying-dimensional model, we devise a state-of-the-art MCMC-type algorithm based on partial collapse. The proposed model and methods are used to investigate an association between daily homicide rates in Cali, Colombia and policies that restrict the hours during which the legal sale of alcoholic beverages is permitted. While simultaneously identifying the latent changes in the baseline homicide rate which correspond to the incidence of sociopolitical events, we explore the effect of policies governing the sale of alcohol on homicide rates and seek a policy that balances the economic and cultural dependencies on alcohol sales to the health of the public.

Decoding and modelling of time series count data using Poisson hidden Markov model and Markov ordinal logistic regression models.

PubMed

Sebastian, Tunny; Jeyaseelan, Visalakshi; Jeyaseelan, Lakshmanan; Anandan, Shalini; George, Sebastian; Bangdiwala, Shrikant I

2018-01-01

Hidden Markov models are stochastic models in which the observations are assumed to follow a mixture distribution, but the parameters of the components are governed by a Markov chain which is unobservable. The issues related to the estimation of Poisson-hidden Markov models in which the observations are coming from mixture of Poisson distributions and the parameters of the component Poisson distributions are governed by an m-state Markov chain with an unknown transition probability matrix are explained here. These methods were applied to the data on Vibrio cholerae counts reported every month for 11-year span at Christian Medical College, Vellore, India. Using Viterbi algorithm, the best estimate of the state sequence was obtained and hence the transition probability matrix. The mean passage time between the states were estimated. The 95% confidence interval for the mean passage time was estimated via Monte Carlo simulation. The three hidden states of the estimated Markov chain are labelled as 'Low', 'Moderate' and 'High' with the mean counts of 1.4, 6.6 and 20.2 and the estimated average duration of stay of 3, 3 and 4 months, respectively. Environmental risk factors were studied using Markov ordinal logistic regression analysis. No significant association was found between disease severity levels and climate components.

Statistical modeling of dental unit water bacterial test kit performance.

PubMed

Cohen, Mark E; Harte, Jennifer A; Stone, Mark E; O'Connor, Karen H; Coen, Michael L; Cullum, Malford E

2007-01-01

While it is important to monitor dental water quality, it is unclear whether in-office test kits provide bacterial counts comparable to the gold standard method (R2A). Studies were conducted on specimens with known bacterial concentrations, and from dental units, to evaluate test kit accuracy across a range of bacterial types and loads. Colony forming units (CFU) were counted for samples from each source, using R2A and two types of test kits, and conformity to Poisson distribution expectations was evaluated. Poisson regression was used to test for effects of source and device, and to estimate rate ratios for kits relative to R2A. For all devices, distributions were Poisson for low CFU/mL when only beige-pigmented bacteria were considered. For higher counts, R2A remained Poisson, but kits exhibited over-dispersion. Both kits undercounted relative to R2A, but the degree of undercounting was reasonably stable. Kits did not grow pink-pigmented bacteria from dental-unit water identified as Methylobacterium rhodesianum. Only one of the test kits provided results with adequate reliability at higher bacterial concentrations. Undercount bias could be estimated for this device and used to adjust test kit results. Insensitivity to methylobacteria spp. is problematic.

Characterization of Nonhomogeneous Poisson Processes Via Moment Conditions.

DTIC Science & Technology

1986-08-01

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

Poisson Mixture Regression Models for Heart Disease Prediction.

PubMed

Mufudza, Chipo; Erol, Hamza

2016-01-01

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

Constructions and classifications of projective Poisson varieties.

PubMed

Pym, Brent

2018-01-01

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

Poisson Mixture Regression Models for Heart Disease Prediction

PubMed Central

Erol, Hamza

2016-01-01

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

Constructions and classifications of projective Poisson varieties

NASA Astrophysics Data System (ADS)

Pym, Brent

2018-03-01

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

A poisson process model for hip fracture risk.

PubMed

Schechner, Zvi; Luo, Gangming; Kaufman, Jonathan J; Siffert, Robert S

2010-08-01

The primary method for assessing fracture risk in osteoporosis relies primarily on measurement of bone mass. Estimation of fracture risk is most often evaluated using logistic or proportional hazards models. Notwithstanding the success of these models, there is still much uncertainty as to who will or will not suffer a fracture. This has led to a search for other components besides mass that affect bone strength. The purpose of this paper is to introduce a new mechanistic stochastic model that characterizes the risk of hip fracture in an individual. A Poisson process is used to model the occurrence of falls, which are assumed to occur at a rate, lambda. The load induced by a fall is assumed to be a random variable that has a Weibull probability distribution. The combination of falls together with loads leads to a compound Poisson process. By retaining only those occurrences of the compound Poisson process that result in a hip fracture, a thinned Poisson process is defined that itself is a Poisson process. The fall rate is modeled as an affine function of age, and hip strength is modeled as a power law function of bone mineral density (BMD). The risk of hip fracture can then be computed as a function of age and BMD. By extending the analysis to a Bayesian framework, the conditional densities of BMD given a prior fracture and no prior fracture can be computed and shown to be consistent with clinical observations. In addition, the conditional probabilities of fracture given a prior fracture and no prior fracture can also be computed, and also demonstrate results similar to clinical data. The model elucidates the fact that the hip fracture process is inherently random and improvements in hip strength estimation over and above that provided by BMD operate in a highly "noisy" environment and may therefore have little ability to impact clinical practice.

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

NASA Astrophysics Data System (ADS)

Wang, Fengwen

2018-05-01

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

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

NASA Astrophysics Data System (ADS)

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

2015-05-01

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

Adjusting for sampling variability in sparse data: geostatistical approaches to disease mapping

PubMed Central

2011-01-01

Background Disease maps of crude rates from routinely collected health data indexed at a small geographical resolution pose specific statistical problems due to the sparse nature of the data. Spatial smoothers allow areas to borrow strength from neighboring regions to produce a more stable estimate of the areal value. Geostatistical smoothers are able to quantify the uncertainty in smoothed rate estimates without a high computational burden. In this paper, we introduce a uniform model extension of Bayesian Maximum Entropy (UMBME) and compare its performance to that of Poisson kriging in measures of smoothing strength and estimation accuracy as applied to simulated data and the real data example of HIV infection in North Carolina. The aim is to produce more reliable maps of disease rates in small areas to improve identification of spatial trends at the local level. Results In all data environments, Poisson kriging exhibited greater smoothing strength than UMBME. With the simulated data where the true latent rate of infection was known, Poisson kriging resulted in greater estimation accuracy with data that displayed low spatial autocorrelation, while UMBME provided more accurate estimators with data that displayed higher spatial autocorrelation. With the HIV data, UMBME performed slightly better than Poisson kriging in cross-validatory predictive checks, with both models performing better than the observed data model with no smoothing. Conclusions Smoothing methods have different advantages depending upon both internal model assumptions that affect smoothing strength and external data environments, such as spatial correlation of the observed data. Further model comparisons in different data environments are required to provide public health practitioners with guidelines needed in choosing the most appropriate smoothing method for their particular health dataset. PMID:21978359

Adjusting for sampling variability in sparse data: geostatistical approaches to disease mapping.

PubMed

Hampton, Kristen H; Serre, Marc L; Gesink, Dionne C; Pilcher, Christopher D; Miller, William C

2011-10-06

Disease maps of crude rates from routinely collected health data indexed at a small geographical resolution pose specific statistical problems due to the sparse nature of the data. Spatial smoothers allow areas to borrow strength from neighboring regions to produce a more stable estimate of the areal value. Geostatistical smoothers are able to quantify the uncertainty in smoothed rate estimates without a high computational burden. In this paper, we introduce a uniform model extension of Bayesian Maximum Entropy (UMBME) and compare its performance to that of Poisson kriging in measures of smoothing strength and estimation accuracy as applied to simulated data and the real data example of HIV infection in North Carolina. The aim is to produce more reliable maps of disease rates in small areas to improve identification of spatial trends at the local level. In all data environments, Poisson kriging exhibited greater smoothing strength than UMBME. With the simulated data where the true latent rate of infection was known, Poisson kriging resulted in greater estimation accuracy with data that displayed low spatial autocorrelation, while UMBME provided more accurate estimators with data that displayed higher spatial autocorrelation. With the HIV data, UMBME performed slightly better than Poisson kriging in cross-validatory predictive checks, with both models performing better than the observed data model with no smoothing. Smoothing methods have different advantages depending upon both internal model assumptions that affect smoothing strength and external data environments, such as spatial correlation of the observed data. Further model comparisons in different data environments are required to provide public health practitioners with guidelines needed in choosing the most appropriate smoothing method for their particular health dataset.

Wavelets, ridgelets, and curvelets for Poisson noise removal.

PubMed

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

2008-07-01

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

Sparsity-based Poisson denoising with dictionary learning.

PubMed

Giryes, Raja; Elad, Michael

2014-12-01

The problem of Poisson denoising appears in various imaging applications, such as low-light photography, medical imaging, and microscopy. In cases of high SNR, several transformations exist so as to convert the Poisson noise into an additive-independent identically distributed. Gaussian noise, for which many effective algorithms are available. However, in a low-SNR regime, these transformations are significantly less accurate, and a strategy that relies directly on the true noise statistics is required. Salmon et al took this route, proposing a patch-based exponential image representation model based on Gaussian mixture model, leading to state-of-the-art results. In this paper, we propose to harness sparse-representation modeling to the image patches, adopting the same exponential idea. Our scheme uses a greedy pursuit with boot-strapping-based stopping condition and dictionary learning within the denoising process. The reconstruction performance of the proposed scheme is competitive with leading methods in high SNR and achieving state-of-the-art results in cases of low SNR.

On-the-fly Numerical Surface Integration for Finite-Difference Poisson-Boltzmann Methods.

PubMed

Cai, Qin; Ye, Xiang; Wang, Jun; Luo, Ray

2011-11-01

Most implicit solvation models require the definition of a molecular surface as the interface that separates the solute in atomic detail from the solvent approximated as a continuous medium. Commonly used surface definitions include the solvent accessible surface (SAS), the solvent excluded surface (SES), and the van der Waals surface. In this study, we present an efficient numerical algorithm to compute the SES and SAS areas to facilitate the applications of finite-difference Poisson-Boltzmann methods in biomolecular simulations. Different from previous numerical approaches, our algorithm is physics-inspired and intimately coupled to the finite-difference Poisson-Boltzmann methods to fully take advantage of its existing data structures. Our analysis shows that the algorithm can achieve very good agreement with the analytical method in the calculation of the SES and SAS areas. Specifically, in our comprehensive test of 1,555 molecules, the average unsigned relative error is 0.27% in the SES area calculations and 1.05% in the SAS area calculations at the grid spacing of 1/2Å. In addition, a systematic correction analysis can be used to improve the accuracy for the coarse-grid SES area calculations, with the average unsigned relative error in the SES areas reduced to 0.13%. These validation studies indicate that the proposed algorithm can be applied to biomolecules over a broad range of sizes and structures. Finally, the numerical algorithm can also be adapted to evaluate the surface integral of either a vector field or a scalar field defined on the molecular surface for additional solvation energetics and force calculations.

Modeling urban coastal flood severity from crowd-sourced flood reports using Poisson regression and Random Forest

NASA Astrophysics Data System (ADS)

Sadler, J. M.; Goodall, J. L.; Morsy, M. M.; Spencer, K.

2018-04-01

Sea level rise has already caused more frequent and severe coastal flooding and this trend will likely continue. Flood prediction is an essential part of a coastal city's capacity to adapt to and mitigate this growing problem. Complex coastal urban hydrological systems however, do not always lend themselves easily to physically-based flood prediction approaches. This paper presents a method for using a data-driven approach to estimate flood severity in an urban coastal setting using crowd-sourced data, a non-traditional but growing data source, along with environmental observation data. Two data-driven models, Poisson regression and Random Forest regression, are trained to predict the number of flood reports per storm event as a proxy for flood severity, given extensive environmental data (i.e., rainfall, tide, groundwater table level, and wind conditions) as input. The method is demonstrated using data from Norfolk, Virginia USA from September 2010 to October 2016. Quality-controlled, crowd-sourced street flooding reports ranging from 1 to 159 per storm event for 45 storm events are used to train and evaluate the models. Random Forest performed better than Poisson regression at predicting the number of flood reports and had a lower false negative rate. From the Random Forest model, total cumulative rainfall was by far the most dominant input variable in predicting flood severity, followed by low tide and lower low tide. These methods serve as a first step toward using data-driven methods for spatially and temporally detailed coastal urban flood prediction.

A comparison of methods for the analysis of binomial clustered outcomes in behavioral research.

PubMed

Ferrari, Alberto; Comelli, Mario

2016-12-01

In behavioral research, data consisting of a per-subject proportion of "successes" and "failures" over a finite number of trials often arise. This clustered binary data are usually non-normally distributed, which can distort inference if the usual general linear model is applied and sample size is small. A number of more advanced methods is available, but they are often technically challenging and a comparative assessment of their performances in behavioral setups has not been performed. We studied the performances of some methods applicable to the analysis of proportions; namely linear regression, Poisson regression, beta-binomial regression and Generalized Linear Mixed Models (GLMMs). We report on a simulation study evaluating power and Type I error rate of these models in hypothetical scenarios met by behavioral researchers; plus, we describe results from the application of these methods on data from real experiments. Our results show that, while GLMMs are powerful instruments for the analysis of clustered binary outcomes, beta-binomial regression can outperform them in a range of scenarios. Linear regression gave results consistent with the nominal level of significance, but was overall less powerful. Poisson regression, instead, mostly led to anticonservative inference. GLMMs and beta-binomial regression are generally more powerful than linear regression; yet linear regression is robust to model misspecification in some conditions, whereas Poisson regression suffers heavily from violations of the assumptions when used to model proportion data. We conclude providing directions to behavioral scientists dealing with clustered binary data and small sample sizes. Copyright © 2016 Elsevier B.V. All rights reserved.

Crustal structure in Ethiopia and Kenya from receiver function analysis: Implications for rift development in eastern Africa

NASA Astrophysics Data System (ADS)

Dugda, Mulugeta T.; Nyblade, Andrew A.; Julia, Jordi; Langston, Charles A.; Ammon, Charles J.; Simiyu, Silas

2005-01-01

Crustal structure in Kenya and Ethiopia has been investigated using receiver function analysis of broadband seismic data to determine the extent to which the Cenozoic rifting and magmatism has modified the thickness and composition of the Proterozoic crust in which the East African rift system developed. Data for this study come from broadband seismic experiments conducted in Ethiopia between 2000 and 2002 and in Kenya between 2001 and 2002. Two methods have been used to analyze the receiver functions, the H-κ method, and direct stacks of the waveforms, yielding consistent results. Crustal thickness to the east of the Kenya rift varies between 39 and 42 km, and Poisson's ratios for the crust vary between 0.24 and 0.27. To the west of the Kenya rift, Moho depths vary between 37 and 38 km, and Poisson's ratios vary between 0.24 and 0.27. These findings support previous studies showing that crust away from the Kenya rift has not been modified extensively by Cenozoic rifting and magmatism. Beneath the Ethiopian Plateau on either side of the Main Ethiopian Rift, crustal thickness ranges from 33 to 44 km, and Poisson's ratios vary from 0.23 to 0.28. Within the Main Ethiopian Rift, Moho depths vary from 27 to 38 km, and Poisson's ratios range from 0.27 to 0.35. A crustal thickness of 25 km and a Poisson's ratio of 0.36 were obtained for a single station in the Afar Depression. These results indicate that the crust beneath the Ethiopian Plateau has not been modified significantly by the Cenozoic rifting and magmatism, even though up to a few kilometers of flood basalts have been added, and that the crust beneath the rifted regions in Ethiopia has been thinned in many places and extensively modified by the addition of mafic rock. The latter finding is consistent with models for rift evolution, suggesting that magmatic segments with the Main Ethiopian Rift, characterized by dike intrusion and Quaternary volcanism, act now as the locus of extension rather than the rift border faults.

A quantum mechanical-Poisson-Boltzmann equation approach for studying charge flow between ions and a dielectric continuum

NASA Astrophysics Data System (ADS)

Gogonea, Valentin; Merz, Kenneth M.

2000-02-01

This paper presents a theoretical model for the investigation of charge transfer between ions and a solvent treated as a dielectric continuum media. The method is a combination of a semiempirical effective Hamiltonian with a modified Poisson-Boltzmann equation which includes charge transfer in the form of a surface charge density positioned at the dielectric interface. The new Poisson-Boltzmann equation together with new boundary conditions results in a new set of equations for the electrostatic potential (or polarization charge densities). Charge transfer adds a new free energy component to the solvation free energy term, which accounts for all interactions between the transferred charge at the dielectric interface, the solute wave function and the solvent polarization charges. Practical calculations on a set of 19 anions and 17 cations demonstrate that charge exchange with a dielectric is present and it is in the range of 0.06-0.4 eu. Furthermore, the pattern of the magnitudes of charge transfer can be related to the acid-base properties of the ions in many cases, but exceptions are also found. Finally, we show that the method leads to an energy decomposition scheme of the total electrostatic energy, which can be used in mechanistic studies on protein and DNA interaction with water.

Quantifying biological samples using Linear Poisson Independent Component Analysis for MALDI-ToF mass spectra

PubMed Central

Deepaisarn, S; Tar, P D; Thacker, N A; Seepujak, A; McMahon, A W

2018-01-01

Abstract Motivation Matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI) facilitates the analysis of large organic molecules. However, the complexity of biological samples and MALDI data acquisition leads to high levels of variation, making reliable quantification of samples difficult. We present a new analysis approach that we believe is well-suited to the properties of MALDI mass spectra, based upon an Independent Component Analysis derived for Poisson sampled data. Simple analyses have been limited to studying small numbers of mass peaks, via peak ratios, which is known to be inefficient. Conventional PCA and ICA methods have also been applied, which extract correlations between any number of peaks, but we argue makes inappropriate assumptions regarding data noise, i.e. uniform and Gaussian. Results We provide evidence that the Gaussian assumption is incorrect, motivating the need for our Poisson approach. The method is demonstrated by making proportion measurements from lipid-rich binary mixtures of lamb brain and liver, and also goat and cow milk. These allow our measurements and error predictions to be compared to ground truth. Availability and implementation Software is available via the open source image analysis system TINA Vision, www.tina-vision.net. Contact paul.tar@manchester.ac.uk Supplementary information Supplementary data are available at Bioinformatics online. PMID:29091994

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

NASA Astrophysics Data System (ADS)

Ofek, Eran O.; Zackay, Barak

2018-04-01

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

Reduction of the discretization stencil of direct forcing immersed boundary methods on rectangular cells: The ghost node shifting method

NASA Astrophysics Data System (ADS)

Picot, Joris; Glockner, Stéphane

2018-07-01

We present an analytical study of discretization stencils for the Poisson problem and the incompressible Navier-Stokes problem when used with some direct forcing immersed boundary methods. This study uses, but is not limited to, second-order discretization and Ghost-Cell Finite-Difference methods. We show that the stencil size increases with the aspect ratio of rectangular cells, which is undesirable as it breaks assumptions of some linear system solvers. To circumvent this drawback, a modification of the Ghost-Cell Finite-Difference methods is proposed to reduce the size of the discretization stencil to the one observed for square cells, i.e. with an aspect ratio equal to one. Numerical results validate this proposed method in terms of accuracy and convergence, for the Poisson problem and both Dirichlet and Neumann boundary conditions. An improvement on error levels is also observed. In addition, we show that the application of the chosen Ghost-Cell Finite-Difference methods to the Navier-Stokes problem, discretized by a pressure-correction method, requires an additional interpolation step. This extra step is implemented and validated through well known test cases of the Navier-Stokes equations.

Unimodularity criteria for Poisson structures on foliated manifolds

NASA Astrophysics Data System (ADS)

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

2018-03-01

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

A 2D forward and inverse code for streaming potential problems

NASA Astrophysics Data System (ADS)

Soueid Ahmed, A.; Jardani, A.; Revil, A.

2013-12-01

The self-potential method corresponds to the passive measurement of the electrical field in response to the occurrence of natural sources of current in the ground. One of these sources corresponds to the streaming current associated with the flow of the groundwater. We can therefore apply the self- potential method to recover non-intrusively some information regarding the groundwater flow. We first solve the forward problem starting with the solution of the groundwater flow problem, then computing the source current density, and finally solving a Poisson equation for the electrical potential. We use the finite-element method to solve the relevant partial differential equations. In order to reduce the number of (petrophysical) model parameters required to solve the forward problem, we introduced an effective charge density tensor of the pore water, which can be determined directly from the permeability tensor for neutral pore waters. The second aspect of our work concerns the inversion of the self-potential data using Tikhonov regularization with smoothness and weighting depth constraints. This approach accounts for the distribution of the electrical resistivity, which can be independently and approximately determined from electrical resistivity tomography. A numerical code, SP2DINV, has been implemented in Matlab to perform both the forward and inverse modeling. Three synthetic case studies are discussed.

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

PubMed

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

1988-06-28

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

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

DOE PAGES

Sanborn, Brett; Song, Bo

2018-06-03

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

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

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

Sanborn, Brett; Song, Bo

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

Investigation of the complex electroviscous effects on electrolyte (single and multiphase) flow in porous medi.

NASA Astrophysics Data System (ADS)

Bolet, A. J. S.; Linga, G.; Mathiesen, J.

2017-12-01

Surface charge is an important control parameter for wall-bounded flow of electrolyte solution. The electroviscous effect has been studied theoretically in model geometries such as infinite capillaries. However, in more complex geometries a quantification of the electroviscous effect is a non-trival task due to strong non-linarites of the underlying equations. In general, one has to rely on numerical methods. Here we present numerical studies of the full three-dimensional steady state Stokes-Poisson-Nernst-Planck problem in order to model electrolyte transport in artificial porous samples. The simulations are performed using the finite element method. From the simulation, we quantity how the electroviscous effect changes the general flow permeability in complex three-dimensional porous media. The porous media we consider are mostly generated artificially by connecting randomly dispersed cylindrical pores. Furthermore, we present results of electric driven two-phase immiscible flow in two dimensions. The simulations are performed by augmenting the above equations with a phase field model to handle and track the interaction between the two fluids (using parameters corresponding to oil-water interfaces, where oil non-polar). In particular, we consider the electro-osmotic effect on imbibition due to charged walls and electrolyte-solution.

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

Structure resonances due to space charge in periodic focusing channels

NASA Astrophysics Data System (ADS)

Li, Chao; Jameson, R. A.

2018-02-01

The Vlasov-Poisson model is one of the most effective methods to study the space charge dominated beam evolution self-consistently in a periodic focusing channel. Since the approach to get the solution with this model is not trivial, previous studies are limited in degenerated conditions, either in smoothed channel (constant focusing) [I. Hofmann, Phys. Rev. E 57, 4713 (1998)] or in alternating gradient focusing channel with equal initial beam emittance condition in the degrees of freedom [I. Hofmann et al., Part. Accel. 13, 145 (1983); Chao Li et al., THOBA02, IPAC2016]. To establish a basis, we intentionally limit this article to the study of the pure transverse periodic focusing lattice with arbitrary initial beam condition, and the same lattice structure in both degrees of freedom, but with possibility of different focusing strengths. This will show the extension of the existing work. The full Hamiltonian is invoked for a pure transverse focusing lattice in various initial beam conditions, revealing different mode structure and additional modes beyond those of the degenerated cases. Application of the extended method to realistic lattices (including longitudinal accelerating elements) and further details will then reveal many new insights, and will be presented in later work.

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

PubMed

Yang, Qingyi; Sharp, Kim A

2006-07-01

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

Application of the Hyper-Poisson Generalized Linear Model for Analyzing Motor Vehicle Crashes.

PubMed

Khazraee, S Hadi; Sáez-Castillo, Antonio Jose; Geedipally, Srinivas Reddy; Lord, Dominique

2015-05-01

The hyper-Poisson distribution can handle both over- and underdispersion, and its generalized linear model formulation allows the dispersion of the distribution to be observation-specific and dependent on model covariates. This study's objective is to examine the potential applicability of a newly proposed generalized linear model framework for the hyper-Poisson distribution in analyzing motor vehicle crash count data. The hyper-Poisson generalized linear model was first fitted to intersection crash data from Toronto, characterized by overdispersion, and then to crash data from railway-highway crossings in Korea, characterized by underdispersion. The results of this study are promising. When fitted to the Toronto data set, the goodness-of-fit measures indicated that the hyper-Poisson model with a variable dispersion parameter provided a statistical fit as good as the traditional negative binomial model. The hyper-Poisson model was also successful in handling the underdispersed data from Korea; the model performed as well as the gamma probability model and the Conway-Maxwell-Poisson model previously developed for the same data set. The advantages of the hyper-Poisson model studied in this article are noteworthy. Unlike the negative binomial model, which has difficulties in handling underdispersed data, the hyper-Poisson model can handle both over- and underdispersed crash data. Although not a major issue for the Conway-Maxwell-Poisson model, the effect of each variable on the expected mean of crashes is easily interpretable in the case of this new model. © 2014 Society for Risk Analysis.

Quasi-Hamiltonian structure and Hojman construction

NASA Astrophysics Data System (ADS)

Carinena, Jose F.; Guha, Partha; Ranada, Manuel F.

2007-08-01

Given a smooth vector field [Gamma] and assuming the knowledge of an infinitesimal symmetry X, Hojman [S. Hojman, The construction of a Poisson structure out of a symmetry and a conservation law of a dynamical system, J. Phys. A Math. Gen. 29 (1996) 667-674] proposed a method for finding both a Poisson tensor and a function H such that [Gamma] is the corresponding Hamiltonian system. In this paper, we approach the problem from geometrical point of view. The geometrization leads to the clarification of several concepts and methods used in Hojman's paper. In particular, the relationship between the nonstandard Hamiltonian structure proposed by Hojman and the degenerate quasi-Hamiltonian structures introduced by Crampin and Sarlet [M. Crampin, W. Sarlet, Bi-quasi-Hamiltonian systems, J. Math. Phys. 43 (2002) 2505-2517] is unveiled in this paper. We also provide some applications of our construction.

LSI arrays for space stations

NASA Technical Reports Server (NTRS)

Gassaway, J. D.

1976-01-01

Two approaches have been taken to study CCD's and some of their fundamental limitations. First a numerical analysis approach has been developed to solve the coupled transport and Poisson's equation for a thorough analysis of charge transfer in a CCD structure. The approach is formulated by treating the minority carriers as a surface distribution at the Si-SiO2 interface and setting up coupled difference equations for the charge and the potential. The SOR method is proposed for solving the two dimensional Poisson's equation for the potential. Methods are suggested for handling the discontinuities to improve convergence. Second, CCD shift registers were fabricated with parameters which should allow complete charge transfer independent of the transfer electrode gap width. A test instrument was designed and constructed which can be used to test this, or any similar, three phase CCD shift register.

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

Rapid computation of directional wellbore drawdown in a confined aquifer via Poisson resummation

NASA Astrophysics Data System (ADS)

Blumenthal, Benjamin J.; Zhan, Hongbin

2016-08-01

We have derived a rapidly computed analytical solution for drawdown caused by a partially or fully penetrating directional wellbore (vertical, horizontal, or slant) via Green's function method. The mathematical model assumes an anisotropic, homogeneous, confined, box-shaped aquifer. Any dimension of the box can have one of six possible boundary conditions: 1) both sides no-flux; 2) one side no-flux - one side constant-head; 3) both sides constant-head; 4) one side no-flux; 5) one side constant-head; 6) free boundary conditions. The solution has been optimized for rapid computation via Poisson Resummation, derivation of convergence rates, and numerical optimization of integration techniques. Upon application of the Poisson Resummation method, we were able to derive two sets of solutions with inverse convergence rates, namely an early-time rapidly convergent series (solution-A) and a late-time rapidly convergent series (solution-B). From this work we were able to link Green's function method (solution-B) back to image well theory (solution-A). We then derived an equation defining when the convergence rate between solution-A and solution-B is the same, which we termed the switch time. Utilizing the more rapidly convergent solution at the appropriate time, we obtained rapid convergence at all times. We have also shown that one may simplify each of the three infinite series for the three-dimensional solution to 11 terms and still maintain a maximum relative error of less than 10-14.