Poisson-Boltzmann versus Size-Modified Poisson-Boltzmann Electrostatics Applied to Lipid Bilayers.
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.
Electrostatic forces in the Poisson-Boltzmann systems.
Xiao, Li; Cai, Qin; Ye, Xiang; Wang, Jun; Luo, Ray
2013-09-07
Continuum modeling of electrostatic interactions based upon numerical solutions of the Poisson-Boltzmann equation has been widely used in structural and functional analyses of biomolecules. A limitation of the numerical strategies is that it is conceptually difficult to incorporate these types of models into molecular mechanics simulations, mainly because of the issue in assigning atomic forces. In this theoretical study, we first derived the Maxwell stress tensor for molecular systems obeying the full nonlinear Poisson-Boltzmann equation. We further derived formulations of analytical electrostatic forces given the Maxwell stress tensor and discussed the relations of the formulations with those published in the literature. We showed that the formulations derived from the Maxwell stress tensor require a weaker condition for its validity, applicable to nonlinear Poisson-Boltzmann systems with a finite number of singularities such as atomic point charges and the existence of discontinuous dielectric as in the widely used classical piece-wise constant dielectric models.
A generalized Poisson and Poisson-Boltzmann solver for electrostatic environments
Fisicaro, G., E-mail: giuseppe.fisicaro@unibas.ch; Goedecker, S. [Department of Physics, University of Basel, Klingelbergstrasse 82, 4056 Basel (Switzerland); Genovese, L. [University of Grenoble Alpes, CEA, INAC-SP2M, L-Sim, F-38000 Grenoble (France); Andreussi, O. [Institute of Computational Science, Università della Svizzera Italiana, Via Giuseppe Buffi 13, CH-6904 Lugano (Switzerland); Theory and Simulations of Materials (THEOS) and National Centre for Computational Design and Discovery of Novel Materials (MARVEL), École Polytechnique Fédérale de Lausanne, Station 12, CH-1015 Lausanne (Switzerland); Marzari, N. [Theory and Simulations of Materials (THEOS) and National Centre for Computational Design and Discovery of Novel Materials (MARVEL), École Polytechnique Fédérale de Lausanne, Station 12, CH-1015 Lausanne (Switzerland)
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.
On space enrichment estimator for nonlinear Poisson-Boltzmann
Randrianarivony, Maharavo
2013-10-01
We consider the mathematical aspect of the nonlinear Poisson-Boltzmann equation which physically governs the ionic interaction between solute and solvent media. The presented a-posteriori estimates can be computed locally in a very efficient manner. The a-posteriori error is based upon hierarchical space enrichment which ensures its efficiency and reliability. A brief survey of the solving of the nonlinear system resulting from the FEM discretization is reported. To corroborate the analysis, we report on a few numerical results for illustrations. We numerically examine some values of the constants encountered in the theoretical study.
Numerical Poisson-Boltzmann Model for Continuum Membrane Systems.
Botello-Smith, Wesley M; Liu, Xingping; Cai, Qin; Li, Zhilin; Zhao, Hongkai; Luo, Ray
2013-01-01
Membrane protein systems are important computational research topics due to their roles in rational drug design. In this study, we developed a continuum membrane model utilizing a level set formulation under the numerical Poisson-Boltzmann framework within the AMBER molecular mechanics suite for applications such as protein-ligand binding affinity and docking pose predictions. Two numerical solvers were adapted for periodic systems to alleviate possible edge effects. Validation on systems ranging from organic molecules to membrane proteins up to 200 residues, demonstrated good numerical properties. This lays foundations for sophisticated models with variable dielectric treatments and second-order accurate modeling of solvation interactions.
Polyelectrolyte Microcapsules: Ion Distributions from a Poisson-Boltzmann Model
Tang, Qiyun; Denton, Alan R.; Rozairo, Damith; Croll, Andrew B.
2014-03-01
Recent experiments have shown that polystyrene-polyacrylic-acid-polystyrene (PS-PAA-PS) triblock copolymers in a solvent mixture of water and toluene can self-assemble into spherical microcapsules. Suspended in water, the microcapsules have a toluene core surrounded by an elastomer triblock shell. The longer, hydrophilic PAA blocks remain near the outer surface of the shell, becoming charged through dissociation of OH functional groups in water, while the shorter, hydrophobic PS blocks form a networked (glass or gel) structure. Within a mean-field Poisson-Boltzmann theory, we model these polyelectrolyte microcapsules as spherical charged shells, assuming different dielectric constants inside and outside the capsule. By numerically solving the nonlinear Poisson-Boltzmann equation, we calculate the radial distribution of anions and cations and the osmotic pressure within the shell as a function of salt concentration. Our predictions, which can be tested by comparison with experiments, may guide the design of microcapsules for practical applications, such as drug delivery. This work was supported by the National Science Foundation under Grant No. DMR-1106331.
Polarizable Atomic Multipole Solutes in a Poisson-Boltzmann Continuum
Schnieders, Michael J.; Baker, Nathan A.; Ren, Pengyu; Ponder, Jay W.
2008-01-01
Modeling the change in the electrostatics of organic molecules upon moving from vacuum into solvent, due to polarization, has long been an interesting problem. In vacuum, experimental values for the dipole moments and polarizabilities of small, rigid molecules are known to high accuracy; however, it has generally been difficult to determine these quantities for a polar molecule in water. A theoretical approach introduced by Onsager used vacuum properties of small molecules, including polarizability, dipole moment and size, to predict experimentally known permittivities of neat liquids via the Poisson equation. Since this important advance in understanding the condensed phase, a large number of computational methods have been developed to study solutes embedded in a continuum via numerical solutions to the Poisson-Boltzmann equation (PBE). Only recently have the classical force fields used for studying biomolecules begun to include explicit polarization in their functional forms. Here we describe the theory underlying a newly developed Polarizable Multipole Poisson-Boltzmann (PMPB) continuum electrostatics model, which builds on the Atomic Multipole Optimized Energetics for Biomolecular Applications (AMOEBA) force field. As an application of the PMPB methodology, results are presented for several small folded proteins studied by molecular dynamics in explicit water as well as embedded in the PMPB continuum. The dipole moment of each protein increased on average by a factor of 1.27 in explicit water and 1.26 in continuum solvent. The essentially identical electrostatic response in both models suggests that PMPB electrostatics offers an efficient alternative to sampling explicit solvent molecules for a variety of interesting applications, including binding energies, conformational analysis, and pKa prediction. Introduction of 150 mM salt lowered the electrostatic solvation energy between 2–13 kcal/mole, depending on the formal charge of the protein, but had only a
Poisson-Boltzmann Calculations: van der Waals or Molecular Surface?
Pang, Xiaodong; Zhou, Huan-Xiang
2013-01-01
The Poisson-Boltzmann equation is widely used for modeling the electrostatics of biomolecules, but the calculation results are sensitive to the choice of the boundary between the low solute dielectric and the high solvent dielectric. The default choice for the dielectric boundary has been the molecular surface, but the use of the van der Waals surface has also been advocated. Here we review recent studies in which the two choices are tested against experimental results and explicit-solvent calculations. The assignment of the solvent high dielectric constant to interstitial voids in the solute is often used as a criticism against the van der Waals surface. However, this assignment may not be as unrealistic as previously thought, since hydrogen exchange and other NMR experiments have firmly established that all interior parts of proteins are transiently accessible to the solvent.
Multilevel Methods for the Poisson-Boltzmann Equation
Holst, Michael Jay
We consider the numerical solution of the Poisson -Boltzmann equation (PBE), a three-dimensional second order nonlinear elliptic partial differential equation arising in biophysics. This problem has several interesting features impacting numerical algorithms, including discontinuous coefficients representing material interfaces, rapid nonlinearities, and three spatial dimensions. Similar equations occur in various applications, including nuclear physics, semiconductor physics, population genetics, astrophysics, and combustion. In this thesis, we study the PBE, discretizations, and develop multilevel-based methods for approximating the solutions of these types of equations. We first outline the physical model and derive the PBE, which describes the electrostatic potential of a large complex biomolecule lying in a solvent. We next study the theoretical properties of the linearized and nonlinear PBE using standard function space methods; since this equation has not been previously studied theoretically, we provide existence and uniqueness proofs in both the linearized and nonlinear cases. We also analyze box-method discretizations of the PBE, establishing several properties of the discrete equations which are produced. In particular, we show that the discrete nonlinear problem is well-posed. We study and develop linear multilevel methods for interface problems, based on algebraic enforcement of Galerkin or variational conditions, and on coefficient averaging procedures. Using a stencil calculus, we show that in certain simplified cases the two approaches are equivalent, with different averaging procedures corresponding to different prolongation operators. We also develop methods for nonlinear problems based on a nonlinear multilevel method, and on linear multilevel methods combined with a globally convergent damped-inexact-Newton method. We derive a necessary and sufficient descent condition for the inexact-Newton direction, enabling the development of extremely
PB-AM: An open-source, fully analytical linear poisson-boltzmann solver
Felberg, Lisa E. [Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley California 94720; Brookes, David H. [Department of Chemistry, University of California Berkeley, Berkeley California 94720; Yap, Eng-Hui [Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx New York 10461; Jurrus, Elizabeth [Division of Computational and Statistical Analytics, Pacific Northwest National Laboratory, Richland Washington 99352; Scientific Computing and Imaging Institute, University of Utah, Salt Lake City Utah 84112; Baker, Nathan A. [Advanced Computing, Mathematics, and Data Division, Pacific Northwest National Laboratory, Richland Washington 99352; Division of Applied Mathematics, Brown University, Providence Rhode Island 02912; Head-Gordon, Teresa [Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley California 94720; Department of Chemistry, University of California Berkeley, Berkeley California 94720; Department of Bioengineering, University of California Berkeley, Berkeley California 94720; Chemical Sciences Division, Lawrence Berkeley National Labs, Berkeley California 94720
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-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.
Bohinc, Klemen; Shrestha, Ahis; Brumen, Milan; May, Sylvio
2012-03-01
In the classical mean-field description of the electric double layer, known as the Poisson-Boltzmann model, ions interact exclusively through their Coulomb potential. Ion specificity can arise through solvent-mediated, nonelectrostatic interactions between ions. We employ the Yukawa pair potential to model the presence of nonelectrostatic interactions. The combination of Yukawa and Coulomb potential on the mean-field level leads to the Poisson-Helmholtz-Boltzmann model, which employs two auxiliary potentials: one electrostatic and the other nonelectrostatic. In the present work we apply the Poisson-Helmholtz-Boltzmann model to ionic mixtures, consisting of monovalent cations and anions that exhibit different Yukawa interaction strengths. As a specific example we consider a single charged surface in contact with a symmetric monovalent electrolyte. From the minimization of the mean-field free energy we derive the Poisson-Boltzmann and Helmholtz-Boltzmann equations. These nonlinear equations can be solved analytically in the weak perturbation limit. This together with numerical solutions in the nonlinear regime suggests an intricate interplay between electrostatic and nonelectrostatic interactions. The structure and free energy of the electric double layer depends sensitively on the Yukawa interaction strengths between the different ion types and on the nonelectrostatic interactions of the mobile ions with the surface.
Structural interactions in ionic liquids linked to higher-order Poisson-Boltzmann equations.
Blossey, R; Maggs, A C; Podgornik, R
2017-06-01
We present a derivation of generalized Poisson-Boltzmann equations starting from classical theories of binary fluid mixtures, employing an approach based on the Legendre transform as recently applied to the case of local descriptions of the fluid free energy. Under specific symmetry assumptions, and in the linearized regime, the Poisson-Boltzmann equation reduces to a phenomenological equation introduced by Bazant et al. [Phys. Rev. Lett. 106, 046102 (2011)]PRLTAO0031-900710.1103/PhysRevLett.106.046102, whereby the structuring near the surface is determined by bulk coefficients.
Ion-Conserving Modified Poisson-Boltzmann Theory Considering a Steric Effect in an Electrolyte
Sugioka, Hideyuki
2016-12-01
The modified Poisson-Nernst-Planck (MPNP) and modified Poisson-Boltzmann (MPB) equations are well known as fundamental equations that consider a steric effect, which prevents unphysical ion concentrations. However, it is unclear whether they are equivalent or not. To clarify this problem, we propose an improved free energy formulation that considers a steric limit with an ion-conserving condition and successfully derive the ion-conserving modified Poisson-Boltzmann (IC-MPB) equations that are equivalent to the MPNP equations. Furthermore, we numerically examine the equivalence by comparing between the IC-MPB solutions obtained by the Newton method and the steady MPNP solutions obtained by the finite-element finite-volume method. A surprising aspect of our finding is that the MPB solutions are much different from the MPNP (IC-MPB) solutions in a confined space. We consider that our findings will significantly contribute to understanding the surface science between solids and liquids.
Xie, Dexuan; Jiang, Yi
2016-10-01
The nonlocal dielectric approach has been studied for more than forty years but only limited to water solvent until the recent work of Xie et al. (2013) [20]. As the development of this recent work, in this paper, a nonlocal modified Poisson-Boltzmann equation (NMPBE) is proposed to incorporate nonlocal dielectric effects into the classic Poisson-Boltzmann equation (PBE) for protein in ionic solvent. The focus of this paper is to present an efficient finite element algorithm and a related software package for solving NMPBE. Numerical results are reported to validate this new software package and demonstrate its high performance for protein molecules. They also show the potential of NMPBE as a better predictor of electrostatic solvation and binding free energies than PBE.
PB-AM: An open-source, fully analytical linear poisson-boltzmann solver.
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.
Beyond Poisson-Boltzmann: fluctuations and fluid structure in a self-consistent theory.
Buyukdagli, S; Blossey, R
2016-09-01
Poisson-Boltzmann (PB) theory is the classic approach to soft matter electrostatics and has been applied to numerous physical chemistry and biophysics problems. Its essential limitations are in its neglect of correlation effects and fluid structure. Recently, several theoretical insights have allowed the formulation of approaches that go beyond PB theory in a systematic way. In this topical review, we provide an update on the developments achieved in the self-consistent formulations of correlation-corrected Poisson-Boltzmann theory. We introduce a corresponding system of coupled non-linear equations for both continuum electrostatics with a uniform dielectric constant, and a structured solvent-a dipolar Coulomb fluid-including non-local effects. While the approach is only approximate and also limited to corrections in the so-called weak fluctuation regime, it allows us to include physically relevant effects, as we show for a range of applications of these equations.
Surface Tension of Acid Solutions: Fluctuations beyond the Non-linear Poisson-Boltzmann Theory
Markovich, Tomer; Podgornik, Rudi
2016-01-01
We extend our previous study of surface tension of ionic solutions and apply it to the case of acids (and salts) with strong ion-surface interactions. These ion-surface interactions yield a non-linear boundary condition with an effective surface charge due to adsorption of ions from the bulk onto the interface. The calculation is done using the loop-expansion technique, where the zero-loop (mean field) corresponds of the non-linear Poisson-Boltzmann equation. The surface tension is obtained analytically to one-loop order, where the mean-field contribution is a modification of the Poisson-Boltzmann surface tension, and the one-loop contribution gives a generalization of the Onsager-Samaras result. Our theory fits well a wide range of different acids and salts, and is in accord with the reverse Hofmeister series for acids.
Beyond Poisson-Boltzmann: fluctuations and fluid structure in a self-consistent theory
Buyukdagli, S.; Blossey, R.
2016-09-01
Poisson-Boltzmann (PB) theory is the classic approach to soft matter electrostatics and has been applied to numerous physical chemistry and biophysics problems. Its essential limitations are in its neglect of correlation effects and fluid structure. Recently, several theoretical insights have allowed the formulation of approaches that go beyond PB theory in a systematic way. In this topical review, we provide an update on the developments achieved in the self-consistent formulations of correlation-corrected Poisson-Boltzmann theory. We introduce a corresponding system of coupled non-linear equations for both continuum electrostatics with a uniform dielectric constant, and a structured solvent—a dipolar Coulomb fluid—including non-local effects. While the approach is only approximate and also limited to corrections in the so-called weak fluctuation regime, it allows us to include physically relevant effects, as we show for a range of applications of these equations.
Slits, plates, and Poisson-Boltzmann theory in a local formulation of nonlocal electrostatics.
Paillusson, Fabien; Blossey, Ralf
2010-11-01
Polar liquids like water carry a characteristic nanometric length scale, the correlation length of orientation polarizations. Continuum theories that can capture this feature commonly run under the name of "nonlocal" electrostatics since their dielectric response is characterized by a scale-dependent dielectric function ε(q), where q is the wave vector; the Poisson(-Boltzmann) equation then turns into an integro-differential equation. Recently, "local" formulations have been put forward for these theories and applied to water, solvated ions, and proteins. We review the local formalism and show how it can be applied to a structured liquid in slit and plate geometries, and solve the Poisson-Boltzmann theory for a charged plate in a structured solvent with counterions. Our results establish a coherent picture of the local version of nonlocal electrostatics and show its ease of use when compared to the original formulation.
Adaptive Finite Element Modeling Techniques for the Poisson-Boltzmann Equation
Holst, Michael; Yu, Zeyun; Zhou, Yongcheng; Zhu, Yunrong
2010-01-01
We develop an efficient and reliable adaptive finite element method (AFEM) for the nonlinear Poisson-Boltzmann equation (PBE). We first examine the regularization technique of Chen, Holst, and Xu; this technique made possible the first a priori pointwise estimates and the first complete solution and approximation theory for the Poisson-Boltzmann equation. It also made possible the first provably convergent discretization of the PBE, and allowed for the development of a provably convergent AFEM for the PBE. However, in practice the regularization turns out to be numerically ill-conditioned. In this article, we examine a second regularization, and establish a number of basic results to ensure that the new approach produces the same mathematical advantages of the original regularization, without the ill-conditioning property. We then design an AFEM scheme based on the new regularized problem, and show that the resulting AFEM scheme is accurate and reliable, by proving a contraction result for the error. This res...
Tjong, Harianto; Zhou, Huang-Xiang
2006-11-28
The Poisson-Boltzmann equation gives the electrostatic free energy of a solute molecule (with dielectric constant epsilon(l)) solvated in a continuum solvent (with dielectric constant epsilon(s)). Here a simple formula is presented that accurately predicts the electrostatic free energy for all combinations of epsilon(l) and epsilon(s) from the calculation on a single set of epsilon(l) and epsilon(s) values.
Analytical solution of the Boltzmann-Poisson equation and its application to MIS tunneling junctions
Zhang Li-Zhi; Wang Zheng-Chuan
2009-01-01
In order to consider quantum transport under the influence of an electron-electron (e-e) interaction in a mesoscopic conductor, the Boltzmann equation and Poisson equation are investigated jointly. The analytical expressions of the distribution function for the Boltzmann equation and the self-consistent average potential concerned with e-e interaction are obtained, and the dielectric function appearing in the self-consistent average potential is naturally generalized beyond the Thomas-Fermi approximation. Then we apply these results to the tunneling junctions of a metal-insulatorsemiconductor (MIS) in which the electrons are accumulated near the interface of the semiconductor, and we find that the e-e interaction plays an important role in the transport procedure of this system. The electronic density, electric current as well as screening Coulombic potential in this case are studied, and we reveal the time and position dependence of these physical quantities explicitly affected by the e-e interaction.
A novel protocol for linearization of the Poisson-Boltzmann equation
Tsekov, R
2014-01-01
A new protocol for linearization of the Poisson-Boltzmann equation is proposed and the resultant electrostatic equation coincides formally with the Debye-Huckel equation, the solution of which is well known for many electrostatic problems. The protocol is examined on the example of electrostatically stabilized nano-bubbles and it is shown that stable nano-bubbles could be present in aqueous solutions of anionic surfactants near the critical temperature, if the surface potential is constant. At constant surface charge non nano-bubbles could exist.
Solution Poisson-Boltzmann equation: Application in the Human Neuron Membrane
Soares, M A G; Cortez, C M
2008-01-01
With already demonstrated in previous work the equations that describe the space dependence of the electric potential are determined by the solution of the equation of Poisson-Boltzmann. In this work we consider these solutions for the membrane of the human neuron, using a model simplified for this structure considering the distribution of electrolytes in each side of the membrane, as well as the effect of glycocalyx and the lipidic bilayer. It was assumed that on both sides of the membrane the charges are homogeneously distributed and that the potential depends only on coordinate z.
A Combined MPI-CUDA Parallel Solution of Linear and Nonlinear Poisson-Boltzmann Equation
Colmenares, José; Galizia, Antonella; Ortiz, Jesús; Clematis, Andrea; Rocchia, Walter
2014-01-01
The Poisson-Boltzmann equation models the electrostatic potential generated by fixed charges on a polarizable solute immersed in an ionic solution. This approach is often used in computational structural biology to estimate the electrostatic energetic component of the assembly of molecular biological systems. In the last decades, the amount of data concerning proteins and other biological macromolecules has remarkably increased. To fruitfully exploit these data, a huge computational power is needed as well as software tools capable of exploiting it. It is therefore necessary to move towards high performance computing and to develop proper parallel implementations of already existing and of novel algorithms. Nowadays, workstations can provide an amazing computational power: up to 10 TFLOPS on a single machine equipped with multiple CPUs and accelerators such as Intel Xeon Phi or GPU devices. The actual obstacle to the full exploitation of modern heterogeneous resources is efficient parallel coding and porting of software on such architectures. In this paper, we propose the implementation of a full Poisson-Boltzmann solver based on a finite-difference scheme using different and combined parallel schemes and in particular a mixed MPI-CUDA implementation. Results show great speedups when using the two schemes, achieving an 18.9x speedup using three GPUs. PMID:25013789
Features of CPB: a Poisson-Boltzmann solver that uses an adaptive Cartesian grid.
Fenley, Marcia O; Harris, Robert C; Mackoy, Travis; Boschitsch, Alexander H
2015-02-05
The capabilities of an adaptive Cartesian grid (ACG)-based Poisson-Boltzmann (PB) solver (CPB) are demonstrated. CPB solves various PB equations with an ACG, built from a hierarchical octree decomposition of the computational domain. This procedure decreases the number of points required, thereby reducing computational demands. Inside the molecule, CPB solves for the reaction-field component (ϕrf ) of the electrostatic potential (ϕ), eliminating the charge-induced singularities in ϕ. CPB can also use a least-squares reconstruction method to improve estimates of ϕ at the molecular surface. All surfaces, which include solvent excluded, Gaussians, and others, are created analytically, eliminating errors associated with triangulated surfaces. These features allow CPB to produce detailed surface maps of ϕ and compute polar solvation and binding free energies for large biomolecular assemblies, such as ribosomes and viruses, with reduced computational demands compared to other Poisson-Boltzmann equation solvers. The reader is referred to http://www.continuum-dynamics.com/solution-mm.html for how to obtain the CPB software. © 2014 Wiley Periodicals, Inc.
Harris, Robert C; Boschitsch, Alexander H; Fenley, Marcia O
2017-08-08
Many researchers compute surface maps of the electrostatic potential (φ) with the Poisson-Boltzmann (PB) equation to relate the structural information obtained from X-ray and NMR experiments to biomolecular functions. Here we demonstrate that the usual method of obtaining these surface maps of φ, by interpolating from neighboring grid points on the solution grid generated by a PB solver, generates large errors because of the large discontinuity in the dielectric constant (and thus in the normal derivative of φ) at the surface. The Cartesian Poisson-Boltzmann solver contains several features that reduce the numerical noise in surface maps of φ: First, CPB introduces additional mesh points at the Cartesian grid/surface intersections where the PB equation is solved. This procedure ensures that the solution for interior mesh points only references nodes on the interior or on the surfaces; similarly for exterior points. Second, for added points on the surface, a second order least-squares reconstruction (LSR) is implemented that analytically incorporates the discontinuities at the surface. LSR is used both during the solution phase to compute φ at the surface and during postprocessing to obtain φ, induced charges, and ionic pressures. Third, it uses an adaptive grid where the finest grid cells are located near the molecular surface.
Surface Tension of Acid Solutions: Fluctuations beyond the Nonlinear Poisson-Boltzmann Theory.
Markovich, Tomer; Andelman, David; Podgornik, Rudi
2017-01-10
We extend our previous study of surface tension of ionic solutions and apply it to acids (and salts) with strong ion-surface interactions, as described by a single adhesivity parameter for the ionic species interacting with the interface. We derive the appropriate nonlinear boundary condition with an effective surface charge due to the adsorption of ions from the bulk onto the interface. The calculation is done using the loop-expansion technique, where the zero loop (mean field) corresponds of the full nonlinear Poisson-Boltzmann equation. The surface tension is obtained analytically to one-loop order, where the mean-field contribution is a modification of the Poisson-Boltzmann surface tension and the one-loop contribution gives a generalization of the Onsager-Samaras result. Adhesivity significantly affects both contributions to the surface tension, as can be seen from the dependence of surface tension on salt concentration for strongly absorbing ions. Comparison with available experimental data on a wide range of different acids and salts allows the fitting of the adhesivity parameter. In addition, it identifies the regime(s) where the hypotheses on which the theory is based are outside their range of validity.
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
Sensitivities to parameterization in the size-modified Poisson-Boltzmann equation.
Harris, Robert C; Boschitsch, Alexander H; Fenley, Marcia O
2014-02-21
Experimental results have demonstrated that the numbers of counterions surrounding nucleic acids differ from those predicted by the nonlinear Poisson-Boltzmann equation, NLPBE. Some studies have fit these data against the ion size in the size-modified Poisson-Boltzmann equation, SMPBE, but the present study demonstrates that other parameters, such as the Stern layer thickness and the molecular surface definition, can change the number of bound ions by amounts comparable to varying the ion size. These parameters will therefore have to be fit simultaneously against experimental data. In addition, the data presented here demonstrate that the derivative, SK, of the electrostatic binding free energy, ΔGel, with respect to the logarithm of the salt concentration is sensitive to these parameters, and experimental measurements of SK could be used to parameterize the model. However, although better values for the Stern layer thickness and ion size and better molecular surface definitions could improve the model's predictions of the numbers of ions around biomolecules and SK, ΔGel itself is more sensitive to parameters, such as the interior dielectric constant, which in turn do not significantly affect the distributions of ions around biomolecules. Therefore, improved estimates of the ion size and Stern layer thickness to use in the SMPBE will not necessarily improve the model's predictions of ΔGel.
How accurate is Poisson-Boltzmann theory for monovalent ions near highly charged interfaces?
Bu, Wei; Vaknin, David; Travesset, Alex
2006-06-20
Surface sensitive synchrotron X-ray scattering studies were performed to obtain the distribution of monovalent ions next to a highly charged interface. A lipid phosphate (dihexadecyl hydrogen-phosphate) was spread as a monolayer at the air-water interface to control surface charge density. Using anomalous reflectivity off and at the L3 Cs+ resonance, we provide spatial counterion (Cs+) distributions next to the negatively charged interfaces. Five decades in bulk concentrations are investigated, demonstrating that the interfacial distribution is strongly dependent on bulk concentration. We show that this is due to the strong binding constant of hydronium H3O+ to the phosphate group, leading to proton-transfer back to the phosphate group and to a reduced surface charge. The increase of Cs+ concentration modifies the contact value potential, thereby causing proton release. This process effectively modifies surface charge density and enables exploration of ion distributions as a function of effective surface charge-density. The experimentally obtained ion distributions are compared to distributions calculated by Poisson-Boltzmann theory accounting for the variation of surface charge density due to proton release and binding. We also discuss the accuracy of our experimental results in discriminating possible deviations from Poisson-Boltzmann theory.
Poisson-Boltzmann thermodynamics of counterions confined by curved hard walls
Šamaj, Ladislav; Trizac, Emmanuel
2016-01-01
We consider a set of identical mobile pointlike charges (counterions) confined to a domain with curved hard walls carrying a uniform fixed surface charge density, the system as a whole being electroneutral. Three domain geometries are considered: a pair of parallel plates, the cylinder, and the sphere. The particle system in thermal equilibrium is assumed to be described by the nonlinear Poisson-Boltzmann theory. While the effectively one-dimensional plates and the two-dimensional cylinder have already been solved, the three-dimensional sphere problem is not integrable. It is shown that the contact density of particles at the charged surface is determined by a first-order Abel differential equation of the second kind which is a counterpart of Enig's equation in the critical theory of gravitation and combustion or explosion. This equation enables us to construct the exact series solutions of the contact density in the regions of small and large surface charge densities. The formalism provides, within the mean-field Poisson-Boltzmann framework, the complete thermodynamics of counterions inside a charged sphere (salt-free system).
A combined MPI-CUDA parallel solution of linear and nonlinear Poisson-Boltzmann equation.
Colmenares, José; Galizia, Antonella; Ortiz, Jesús; Clematis, Andrea; Rocchia, Walter
2014-01-01
The Poisson-Boltzmann equation models the electrostatic potential generated by fixed charges on a polarizable solute immersed in an ionic solution. This approach is often used in computational structural biology to estimate the electrostatic energetic component of the assembly of molecular biological systems. In the last decades, the amount of data concerning proteins and other biological macromolecules has remarkably increased. To fruitfully exploit these data, a huge computational power is needed as well as software tools capable of exploiting it. It is therefore necessary to move towards high performance computing and to develop proper parallel implementations of already existing and of novel algorithms. Nowadays, workstations can provide an amazing computational power: up to 10 TFLOPS on a single machine equipped with multiple CPUs and accelerators such as Intel Xeon Phi or GPU devices. The actual obstacle to the full exploitation of modern heterogeneous resources is efficient parallel coding and porting of software on such architectures. In this paper, we propose the implementation of a full Poisson-Boltzmann solver based on a finite-difference scheme using different and combined parallel schemes and in particular a mixed MPI-CUDA implementation. Results show great speedups when using the two schemes, achieving an 18.9x speedup using three GPUs.
A Combined MPI-CUDA Parallel Solution of Linear and Nonlinear Poisson-Boltzmann Equation
José Colmenares
2014-01-01
Full Text Available The Poisson-Boltzmann equation models the electrostatic potential generated by fixed charges on a polarizable solute immersed in an ionic solution. This approach is often used in computational structural biology to estimate the electrostatic energetic component of the assembly of molecular biological systems. In the last decades, the amount of data concerning proteins and other biological macromolecules has remarkably increased. To fruitfully exploit these data, a huge computational power is needed as well as software tools capable of exploiting it. It is therefore necessary to move towards high performance computing and to develop proper parallel implementations of already existing and of novel algorithms. Nowadays, workstations can provide an amazing computational power: up to 10 TFLOPS on a single machine equipped with multiple CPUs and accelerators such as Intel Xeon Phi or GPU devices. The actual obstacle to the full exploitation of modern heterogeneous resources is efficient parallel coding and porting of software on such architectures. In this paper, we propose the implementation of a full Poisson-Boltzmann solver based on a finite-difference scheme using different and combined parallel schemes and in particular a mixed MPI-CUDA implementation. Results show great speedups when using the two schemes, achieving an 18.9x speedup using three GPUs.
Majee, Arghya; Dietrich, S
2016-01-01
The effective electrostatic interaction between a pair of colloids, both of them located close to each other at an electrolyte interface, is studied by employing the full, nonlinear Poisson-Boltzmann (PB) theory within classical density functional theory. Using a simplified yet appropriate model, all contributions to the effective interaction are obtained exactly, albeit numerically. The comparison between our results and those obtained within linearized PB theory reveals that the latter overestimates these contributions significantly at short inter-particle separations. Whereas the surface contributions to the linear and the nonlinear PB results differ only quantitatively, the line contributions show qualitative differences at short separations. Moreover, a dependence of the line contribution on the solvation properties of the two adjacent fluids is found, which is absent within the linear theory. Our results are expected to enrich the understanding of effective interfacial interactions between colloids.
Langevin Poisson-Boltzmann equation: point-like ions and water dipoles near a charged surface.
Gongadze, Ekaterina; van Rienen, Ursula; Kralj-Iglič, Veronika; Iglič, Aleš
2011-06-01
Water ordering near a charged membrane surface is important for many biological processes such as binding of ligands to a membrane or transport of ions across it. In this work, the mean-field Poisson-Boltzmann theory for point-like ions, describing an electrolyte solution in contact with a planar charged surface, is modified by including the orientational ordering of water. Water molecules are considered as Langevin dipoles, while the number density of water is assumed to be constant everywhere in the electrolyte solution. It is shown that the dielectric permittivity of an electrolyte close to a charged surface is decreased due to the increased orientational ordering of water dipoles. The dielectric permittivity close to the charged surface is additionally decreased due to the finite size of ions and dipoles.
Mirzadeh, Mohammad; Squires, Todd; Gibou, Frederic
2010-11-01
We present a finite difference discretization of the non-linear Poisson-Boltzmann (PB) equation over complex geometries that has second order accurracy. The level-set method is adopted to represent the interface and Octree (in three dimensions) or Quadtree (in two dimensions) data stuructures are used to generate adaptive grids. Such an approach garanties that the finest grid resolution is located near the interface where EDL forms and creates very large electric field. Several numerical experiments are carried which indicate the second order accuracy both in the case of Dirichlet and Neumann boundary conditions in L2 and L∞ norms. Finally, we use our method to study the electrostatic interaction of double layers between charged particles in an unbounded bulk electrolyte as well as in a channel where the channel width is of the order of Debye length.
Ambia-Garrido, Joaquin; Montgomery Pettitt, Bernard
2007-10-01
The change in some thermodynamic quantities such as Gibbs' free energy, entropy and enthalpy of the binding of a particle tethered to a surface or particle are analytically calculated. These particles are considered ellipsoids and submerged in a liquid. The ionic strength of the media allows the linearized version of the Poisson-Boltzmann equation (from the theory of the double layer interaction) to properly describe the interactions between an ion penetrable spheroid and a hard plate. We believe that this is an adequate model for a DNA chip and the predicted electrostatic effects suggest the feasibility of electronic control and detection of DNA hybridization and design of chips, avoiding the DNA folding problem.
Ambia-Garrido, Joaquin; Pettitt, Montgomery
2008-03-01
The change in some thermodynamic quantities such as Gibbs' free energy, entropy and enthalpy of the binding of a particle tethered to a surface or particle are analytically calculated. These particles are considered ellipsoids and submerged in a liquid. The ionic strength of the media allows the linearized version of the Poisson-Boltzmann equation (from the theory of the double layer interaction) to properly describe the interactions between an ion penetrable spheroid and a hard plate. We believe that this is an adequate model for a DNA chip and the predicted electrostatic effects suggest the feasibility of electronic control and detection of DNA hybridization and design of chips underline avoiding the DNA folding problem.
Accurate, robust and reliable calculations of Poisson-Boltzmann solvation energies
Wang, Bao
2016-01-01
Developing accurate solvers for the Poisson Boltzmann (PB) model is the first step to make the PB model suitable for implicit solvent simulation. Reducing the grid size influence on the performance of the solver benefits to increasing the speed of solver and providing accurate electrostatics analysis for solvated molecules. In this work, we explore the accurate coarse grid PB solver based on the Green's function treatment of the singular charges, matched interface and boundary (MIB) method for treating the geometric singularities, and posterior electrostatic potential field extension for calculating the reaction field energy. We made our previous PB software, MIBPB, robust and provides almost grid size independent reaction field energy calculation. Large amount of the numerical tests verify the grid size independence merit of the MIBPB software. The advantage of MIBPB software directly make the acceleration of the PB solver from the numerical algorithm instead of utilization of advanced computer architectures...
Analytical estimation of effective charges at saturation in Poisson-Boltzmann cell models
Trizac, E; Bocquet, L
2003-01-01
We propose a simple approximation scheme for computing the effective charges of highly charged colloids (spherical or cylindrical with infinite length). Within non-linear Poisson-Boltzmann theory, we start from an expression for the effective charge in the infinite-dilution limit which is asymptotically valid for large salt concentrations; this result is then extended to finite colloidal concentration, approximating the salt partitioning effect which relates the salt content in the suspension to that of a dialysing reservoir. This leads to an analytical expression for the effective charge as a function of colloid volume fraction and salt concentration. These results compare favourably with the effective charges at saturation (i.e. in the limit of large bare charge) computed numerically following the standard prescription proposed by Alexander et al within the cell model.
Antosiewicz, Jan M; Shugar, David
2011-11-01
All molecules can be viewed as either discrete or continuous assemblies of electric charges, and electrostatics plays a major role in intermolecular and intramolecular interactions. Moreover, charge distribution within molecules may fluctuate due to the presence of ionizable groups capable of exchanging protons with the environment, leading to pH-dependence of phenomena involving such molecules. Electrostatic aspects of complex shapes and environments of biological molecules, in vitro and in vivo, are relatively well amenable to treatment by Poisson-Boltzmann models, which are attractive in that they possess a clear physical meaning, and can be readily solved by several mathematically sound methods. Here we describe applications of these models to obtain valuable insights into some biologically important pH-dependent properties of biomolecules, such as stability, binding of ligands (including potential drugs), enzymatic activity, conformational transitions, membrane transport and viral entry.
On-the-fly Numerical Surface Integration for Finite-Difference Poisson-Boltzmann Methods.
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.
ADAPTIVE FINITE ELEMENT MODELING TECHNIQUES FOR THE POISSON-BOLTZMANN EQUATION
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
A Fast and Robust Poisson-Boltzmann Solver Based on Adaptive Cartesian Grids
Boschitsch, Alexander H.; Fenley, Marcia O.
2011-01-01
An adaptive Cartesian grid (ACG) concept is presented for the fast and robust numerical solution of the 3D Poisson-Boltzmann Equation (PBE) governing the electrostatic interactions of large-scale biomolecules and highly charged multi-biomolecular assemblies such as ribosomes and viruses. The ACG offers numerous advantages over competing grid topologies such as regular 3D lattices and unstructured grids. For very large biological molecules and multi-biomolecule assemblies, the total number of grid-points is several orders of magnitude less than that required in a conventional lattice grid used in the current PBE solvers thus allowing the end user to obtain accurate and stable nonlinear PBE solutions on a desktop computer. Compared to tetrahedral-based unstructured grids, ACG offers a simpler hierarchical grid structure, which is naturally suited to multigrid, relieves indirect addressing requirements and uses fewer neighboring nodes in the finite difference stencils. Construction of the ACG and determination of the dielectric/ionic maps are straightforward, fast and require minimal user intervention. Charge singularities are eliminated by reformulating the problem to produce the reaction field potential in the molecular interior and the total electrostatic potential in the exterior ionic solvent region. This approach minimizes grid-dependency and alleviates the need for fine grid spacing near atomic charge sites. The technical portion of this paper contains three parts. First, the ACG and its construction for general biomolecular geometries are described. Next, a discrete approximation to the PBE upon this mesh is derived. Finally, the overall solution procedure and multigrid implementation are summarized. Results obtained with the ACG-based PBE solver are presented for: (i) a low dielectric spherical cavity, containing interior point charges, embedded in a high dielectric ionic solvent – analytical solutions are available for this case, thus allowing rigorous
AQUASOL: An efficient solver for the dipolar Poisson-Boltzmann-Langevin equation.
Koehl, Patrice; Delarue, Marc
2010-02-14
The Poisson-Boltzmann (PB) formalism is among the most popular approaches to modeling the solvation of molecules. It assumes a continuum model for water, leading to a dielectric permittivity that only depends on position in space. In contrast, the dipolar Poisson-Boltzmann-Langevin (DPBL) formalism represents the solvent as a collection of orientable dipoles with nonuniform concentration; this leads to a nonlinear permittivity function that depends both on the position and on the local electric field at that position. The differences in the assumptions underlying these two models lead to significant differences in the equations they generate. The PB equation is a second order, elliptic, nonlinear partial differential equation (PDE). Its response coefficients correspond to the dielectric permittivity and are therefore constant within each subdomain of the system considered (i.e., inside and outside of the molecules considered). While the DPBL equation is also a second order, elliptic, nonlinear PDE, its response coefficients are nonlinear functions of the electrostatic potential. Many solvers have been developed for the PB equation; to our knowledge, none of these can be directly applied to the DPBL equation. The methods they use may adapt to the difference; their implementations however are PBE specific. We adapted the PBE solver originally developed by Holst and Saied [J. Comput. Chem. 16, 337 (1995)] to the problem of solving the DPBL equation. This solver uses a truncated Newton method with a multigrid preconditioner. Numerical evidences suggest that it converges for the DPBL equation and that the convergence is superlinear. It is found however to be slow and greedy in memory requirement for problems commonly encountered in computational biology and computational chemistry. To circumvent these problems, we propose two variants, a quasi-Newton solver based on a simplified, inexact Jacobian and an iterative self-consistent solver that is based directly on the PBE
The Ionic Atmosphere around A-RNA: Poisson-Boltzmann and Molecular Dynamics Simulations
Kirmizialtin, Serdal; Silalahi, Alexander R.J.; Elber, Ron; Fenley, Marcia O.
2012-01-01
The distributions of different cations around A-RNA are computed by Poisson-Boltzmann (PB) equation and replica exchange molecular dynamics (MD). Both the nonlinear PB and size-modified PB theories are considered. The number of ions bound to A-RNA, which can be measured experimentally, is well reproduced in all methods. On the other hand, the radial ion distribution profiles show differences between MD and PB. We showed that PB results are sensitive to ion size and functional form of the solvent dielectric region but not the solvent dielectric boundary definition. Size-modified PB agrees with replica exchange molecular dynamics much better than nonlinear PB when the ion sizes are chosen from atomistic simulations. The distribution of ions 14 Å away from the RNA central axis are reasonably well reproduced by size-modified PB for all ion types with a uniform solvent dielectric model and a sharp dielectric boundary between solvent and RNA. However, this model does not agree with MD for shorter distances from the A-RNA. A distance-dependent solvent dielectric function proposed by another research group improves the agreement for sodium and strontium ions, even for shorter distances from the A-RNA. However, Mg2+ distributions are still at significant variances for shorter distances. PMID:22385854
Accurate, robust, and reliable calculations of Poisson-Boltzmann binding energies.
Nguyen, Duc D; Wang, Bao; Wei, Guo-Wei
2017-05-15
Poisson-Boltzmann (PB) model is one of the most popular implicit solvent models in biophysical modeling and computation. The ability of providing accurate and reliable PB estimation of electrostatic solvation free energy, ΔGel, and binding free energy, ΔΔGel, is important to computational biophysics and biochemistry. In this work, we investigate the grid dependence of our PB solver (MIBPB) with solvent excluded surfaces for estimating both electrostatic solvation free energies and electrostatic binding free energies. It is found that the relative absolute error of ΔGel obtained at the grid spacing of 1.0 Å compared to ΔGel at 0.2 Å averaged over 153 molecules is less than 0.2%. Our results indicate that the use of grid spacing 0.6 Å ensures accuracy and reliability in ΔΔGel calculation. In fact, the grid spacing of 1.1 Å appears to deliver adequate accuracy for high throughput screening. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.
Poisson-Boltzmann model of electrolytes containing uniformly charged spherical nanoparticles.
Bohinc, Klemen; Volpe Bossa, Guilherme; Gavryushov, Sergei; May, Sylvio
2016-12-21
Like-charged macromolecules typically repel each other in aqueous solutions that contain small mobile ions. The interaction tends to turn attractive if mobile ions with spatially extended charge distributions are added. Such systems can be modeled within the mean-field Poisson-Boltzmann formalism by explicitly accounting for charge-charge correlations within the spatially extended ions. We consider an aqueous solution that contains a mixture of spherical nanoparticles with uniform surface charge density and small mobile salt ions, sandwiched between two like-charged planar surfaces. We perform the minimization of an appropriate free energy functional, which leads to a non-linear integral-differential equation for the electrostatic potential that we solve numerically and compare with predictions from Monte Carlo simulations. Nanoparticles with uniform surface charge density are contrasted with nanoparticles that have all their charges relocated at the center. Our mean-field model predicts that only the former (especially when large and highly charged particles) but not the latter are able to mediate attractive interactions between like-charged planar surfaces. We also demonstrate that at high salt concentration attractive interactions between like-charged planar surfaces turn into repulsion.
A GPU-accelerated Direct-sum Boundary Integral Poisson-Boltzmann Solver
Geng, Weihua
2013-01-01
In this paper, we present a GPU-accelerated direct-sum boundary integral method to solve the linear Poisson-Boltzmann (PB) equation. In our method, a well-posed boundary integral formulation is used to ensure the fast convergence of Krylov subspace based linear algebraic solver such as the GMRES. The molecular surfaces are discretized with flat triangles and centroid collocation. To speed up our method, we take advantage of the parallel nature of the boundary integral formulation and parallelize the schemes within CUDA shared memory architecture on GPU. The schemes use only $11N+6N_c$ size-of-double device memory for a biomolecule with $N$ triangular surface elements and $N_c$ partial charges. Numerical tests of these schemes show well-maintained accuracy and fast convergence. The GPU implementation using one GPU card (Nvidia Tesla M2070) achieves 120-150X speed-up to the implementation using one CPU (Intel L5640 2.27GHz). With our approach, solving PB equations on well-discretized molecular surfaces with up ...
Lu, Benzhuo; Cheng, Xiaolin; Huang, Jingfang; McCammon, J. Andrew
2013-11-01
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 the 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. 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 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.
Tamashiro, M. N.; Schiessel, H.
2003-07-01
The Poisson-Boltzmann (PB) spherical Wigner-Seitz cell model—introduced to theoretically describe suspensions of spherical charged colloidal particles—is investigated at the nonlinear and linearized levels. The linearization of the mean-field PB functional yields linearized Debye-Hückel-type equations agreeing asymptotically with the nonlinear PB results in the weak-coupling (high-temperature) limit. Both the canonical (fixed number of microions) as well as the semigrand-canonical (in contact with an infinite salt reservoir) cases are considered and discussed in a unified linearized framework. In disagreement with the exact nonlinear PB solution inside a Wigner-Seitz cell, the linearized theory predicts the occurrence of a thermodynamical instability with an associated phase separation of the homogeneous suspension into dilute (gas) and dense (liquid) phases, being thus a spurious result of the linearization. We show that these artifacts, although thermodynamically consistent with quadratic expansions of the nonlinear functional and osmotic pressure, may be traced back to the nonfulfillment of the underlying assumptions of the linearization. This raises questions about the reliability of the prediction of gas/liquid-like phase separation in deionized aqueous suspensions of charged colloids mediated by monovalent counterions obtained by linearized theories.
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.
Ion strength limit of computed excess functions based on the linearized Poisson-Boltzmann equation.
Fraenkel, Dan
2015-12-05
The linearized Poisson-Boltzmann (L-PB) equation is examined for its κ-range of validity (κ, Debye reciprocal length). This is done for the Debye-Hückel (DH) theory, i.e., using a single ion size, and for the SiS treatment (D. Fraenkel, Mol. Phys. 2010, 108, 1435), which extends the DH theory to the case of ion-size dissimilarity (therefore dubbed DH-SiS). The linearization of the PB equation has been claimed responsible for the DH theory's failure to fit with experiment at > 0.1 m; but DH-SiS fits with data of the mean ionic activity coefficient, γ± (molal), against m, even at m > 1 (κ > 0.33 Å(-1) ). The SiS expressions combine the overall extra-electrostatic potential energy of the smaller ion, as central ion-Ψa>b (κ), with that of the larger ion, as central ion-Ψb>a (κ); a and b are, respectively, the counterion and co-ion distances of closest approach. Ψa>b and Ψb>a are derived from the L-PB equation, which appears to conflict with their being effective up to moderate electrolyte concentrations (≈1 m). However, the L-PB equation can be valid up to κ ≥ 1.3 Å(-1) if one abandons the 1/κ criterion for its effectiveness and, instead, use, as criterion, the mean-field electrostatic interaction potential of the central ion with its ion cloud, at a radial distance dividing the cloud charge into two equal parts. The DH theory's failure is, thus, not because of using the L-PB equation; the lethal approximation is assigning a single size to the positive and negative ions. © 2015 Wiley Periodicals, Inc.
Dipolar Poisson-Boltzmann approach to ionic solutions: a mean field and loop expansion analysis.
Levy, Amir; Andelman, David; Orland, Henri
2013-10-28
We study the variation of the dielectric response of ionic aqueous solutions as function of their ionic strength. The effect of salt on the dielectric constant appears through the coupling between ions and dipolar water molecules. On a mean-field level, we account for any internal charge distribution of particles. The dipolar degrees of freedom are added to the ionic ones and result in a generalization of the Poisson-Boltzmann (PB) equation called the Dipolar PB (DPB). By looking at the DPB equation around a fixed point-like ion, a closed-form formula for the dielectric constant is obtained. We express the dielectric constant using the "hydration length" that characterizes the hydration shell of dipoles around ions, and thus the strength of the dielectric decrement. The DPB equation is then examined for three additional cases: mixture of solvents, polarizable medium, and ions of finite size. Employing field-theoretical methods, we expand the Gibbs free-energy to first order in a loop expansion and calculate self-consistently the dielectric constant. For pure water, the dipolar fluctuations represent an important correction to the mean-field value and good agreement with the water dielectric constant is obtained. For ionic solutions we predict analytically the dielectric decrement that depends on the ionic strength in a nonlinear way. Our prediction fits rather well a large range of concentrations for different salts using only one fit parameter related to the size of ions and dipoles. A linear dependence of the dielectric constant on the salt concentration is observed at low salinity, and a noticeable deviation from linearity can be seen for ionic strength above 1 M, in agreement with experiments.
Sharma, P; Mišković, Z L
2015-10-07
We present a model describing the electrostatic interactions across a structure that consists of a single layer of graphene with large area, lying above an oxide substrate of finite thickness, with its surface exposed to a thick layer of liquid electrolyte containing salt ions. Our goal is to analyze the co-operative screening of the potential fluctuation in a doped graphene due to randomness in the positions of fixed charged impurities in the oxide by the charge carriers in graphene and by the mobile ions in the diffuse layer of the electrolyte. In order to account for a possibly large potential drop in the diffuse later that may arise in an electrolytically gated graphene, we use a partially linearized Poisson-Boltzmann (PB) model of the electrolyte, in which we solve a fully nonlinear PB equation for the surface average of the potential in one dimension, whereas the lateral fluctuations of the potential in graphene are tackled by linearizing the PB equation about the average potential. In this way, we are able to describe the regime of equilibrium doping of graphene to large densities for arbitrary values of the ion concentration without restrictions to the potential drop in the electrolyte. We evaluate the electrostatic Green's function for the partially linearized PB model, which is used to express the screening contributions of the graphene layer and the nearby electrolyte by means of an effective dielectric function. We find that, while the screened potential of a single charged impurity at large in-graphene distances exhibits a strong dependence on the ion concentration in the electrolyte and on the doping density in graphene, in the case of a spatially correlated two-dimensional ensemble of impurities, this dependence is largely suppressed in the autocovariance of the fluctuating potential.
Chakavorty, Arghya; Li, Lin; Alexov, Emil
2016-10-30
Macromolecular interactions are essential for understanding numerous biological processes and are typically characterized by the binding free energy. Important component of the binding free energy is the electrostatics, which is frequently modeled via the solutions of the Poisson-Boltzmann Equations (PBE). However, numerous works have shown that the electrostatic component (ΔΔGelec ) of binding free energy is very sensitive to the parameters used and modeling protocol. This prompted some researchers to question the robustness of PBE in predicting ΔΔGelec . We argue that the sensitivity of the absolute ΔΔGelec calculated with PBE using different input parameters and definitions does not indicate PBE deficiency, rather this is what should be expected. We show how the apparent sensitivity should be interpreted in terms of the underlying changes in several numerous and physical parameters. We demonstrate that PBE approach is robust within each considered force field (CHARMM-27, AMBER-94, and OPLS-AA) once the corresponding structures are energy minimized. This observation holds despite of using two different molecular surface definitions, pointing again that PBE delivers consistent results within particular force field. The fact that PBE delivered ΔΔGelec values may differ if calculated with different modeling protocols is not a deficiency of PBE, but natural results of the differences of the force field parameters and potential functions for energy minimization. In addition, while the absolute ΔΔGelec values calculated with different force field differ, their ordering remains practically the same allowing for consistent ranking despite of the force field used. © 2016 Wiley Periodicals, Inc.
Frydel, Derek
2011-06-21
We incorporate ion polarizabilities into the Poisson-Boltzmann equation by modifying the effective dielectric constant and the Boltzmann distribution of ions. The extent of the polarizability effects is controlled by two parameters, γ(1) and γ(2); γ(1) determines the polarization effects in a dilute system and γ(2) regulates the dependence of the polarizability effects on the concentration of ions. For a polarizable ion in an aqueous solution γ(1) ≈ 0.01 and the polarizability effects are negligible. The conditions where γ(1) and/or γ(2) are large and the polarizability is relevant involve the low dielectric constant media, high surface charge, and/or large ionic concentrations. © 2011 American Institute of Physics
Bajaj, Chandrajit; Chen, Shun-Chuan; Rand, Alexander
2011-01-01
In order to compute polarization energy of biomolecules, we describe a boundary element approach to solving the linearized Poisson-Boltzmann equation. Our approach combines several important features including the derivative boundary formulation of the problem and a smooth approximation of the molecular surface based on the algebraic spline molecular surface. State of the art software for numerical linear algebra and the kernel independent fast multipole method is used for both simplicity and efficiency of our implementation. We perform a variety of computational experiments, testing our method on a number of actual proteins involved in molecular docking and demonstrating the effectiveness of our solver for computing molecular polarization energy. PMID:21660123
Wang, Jun; Cai, Qin; Li, Zhi-Lin; Zhao, Hong-Kai; Luo, Ray
2009-01-01
Violation of energy conservation in Poisson-Boltzmann molecular dynamics, due to the limited accuracy and precision of numerical methods, is a major bottleneck preventing its wide adoption in biomolecular simulations. We explored the ideas of enforcing interface conditions by the immerse interface method and of removing charge singularity to improve the finite-difference methods. Our analysis of these ideas on an analytical test system shows significant improvement in both energies and forces. Our analysis further indicates the need for more accurate force calculation, especially the boundary force calculation. PMID:20098487
Ying, Jinyong
2016-01-01
The size-modified Poisson-Boltzmann equation (SMPBE) is one important variant of the popular dielectric model, the Poisson-Boltzmann equation (PBE), to reflect ionic size effects in the prediction of electrostatics for a biomolecule in an ionic solvent. In this paper, a new SMPBE hybrid solver is developed using a solution decomposition, the Schwartz's overlapped domain decomposition, finite element, and finite difference. It is then programmed as a software package in C, Fortran, and Python based on the state-of-the-art finite element library DOLFIN from the FEniCS project. This software package is well validated on a Born ball model with analytical solution and a dipole model with a known physical properties. Numerical results on six proteins with different net charges demonstrate its high performance. Finally, this new SMPBE hybrid solver is shown to be numerically stable and convergent in the calculation of electrostatic solvation free energy for 216 biomolecules and binding free energy for a DNA-drug com...
de Carvalho, Sidney Jurado; Fenley, Márcia O; da Silva, Fernando Luís Barroso
2008-12-25
Electrostatic interactions are one of the key driving forces for protein-ligands complexation. Different levels for the theoretical modeling of such processes are available on the literature. Most of the studies on the Molecular Biology field are performed within numerical solutions of the Poisson-Boltzmann Equation and the dielectric continuum models framework. In such dielectric continuum models, there are two pivotal questions: (a) how the protein dielectric medium should be modeled, and (b) what protocol should be used when solving this effective Hamiltonian. By means of Monte Carlo (MC) and Poisson-Boltzmann (PB) calculations, we define the applicability of the PB approach with linear and nonlinear responses for macromolecular electrostatic interactions in electrolyte solution, revealing some physical mechanisms and limitations behind it especially due the raise of both macromolecular charge and concentration out of the strong coupling regime. A discrepancy between PB and MC for binding constant shifts is shown and explained in terms of the manner PB approximates the excess chemical potentials of the ligand, and not as a consequence of the nonlinear thermal treatment and/or explicit ion-ion interactions as it could be argued. Our findings also show that the nonlinear PB predictions with a low dielectric response well reproduce the pK shifts calculations carried out with an uniform dielectric model. This confirms and completes previous results obtained by both MC and linear PB calculations.
Lahiri, T.; Pal Majumder, T.; Ghosh, N. K.
2014-07-01
Commercialization of ferroelectric liquid crystal displays (FLCDs) suffers from mechanical and electro-convective instabilities. Impurity ions play a pivotal role in the latter case, and therefore we developed a mean-field type model to understand the complex role of space charges, particularly ions in a ferroelectric liquid crystal. Considering an effective ion-chirality relation, we obtained a modified Poisson-Boltzmann equation for ions dissolved into a chiral solvent like the ferroelectric smectic phase. A nonuniform director profile induced by the mean electrostatic potential of the ions is then calculated by solving an Euler-Lagrange equation for a helically twisted smectic state. A combination of effects resulting from molecular chirality and an electrostatically driven twist created by the ions seems to produce this nonuniform fluctuation in the director orientation. Finally, both theoretical and experimental points of view are presented on the prediction of this mean-field model.
Generalized Poisson-Boltzmann Equation Taking into Account Ionic Interaction and Steric Effects
刘新敏; 李航; 李睿; 田锐; 许晨阳
2012-01-01
Generalized Poisson l3oltzmann equation which takes into account both ionic interaction in bulk solution and steric effects of adsorbed ions has been suggested. We found that, for inorganic cations adsorption on negatively charged surface, the steric effect is not significant for surface charge density 〈 0.0032 C/dm2, while the ionic interaction is an important effect for electrolyte concentration 〉 0.15 tool/1 in bulk solution. We conclude that for most actual cases the original PB equation can give reliable result in describing inorganic cation adsorption.
Canonical enhancement as a result of Poisson distribution
Biro, T S
2002-01-01
We point out that a certain finite size effect in heavy ion physics, the canonical enhancement, is based on the difference of conservation constrained pair statistics for Poisson and Gauss distributions, respectively. Consequently it should occur in a wide range of phenomena, whenever comparing rare and frequent events.
Decherchi, Sergio; Colmenares, José; Catalano, Chiara Eva; Spagnuolo, Michela; Alexov, Emil; Rocchia, Walter
2013-01-01
The definition of a molecular surface which is physically sound and computationally efficient is a very interesting and long standing problem in the implicit solvent continuum modeling of biomolecular systems as well as in the molecular graphics field. In this work, two molecular surfaces are evaluated with respect to their suitability for electrostatic computation as alternatives to the widely used Connolly-Richards surface: the blobby surface, an implicit Gaussian atom centered surface, and the skin surface. As figures of merit, we considered surface differentiability and surface area continuity with respect to atom positions, and the agreement with explicit solvent simulations. Geometric analysis seems to privilege the skin to the blobby surface, and points to an unexpected relationship between the non connectedness of the surface, caused by interstices in the solute volume, and the surface area dependence on atomic centers. In order to assess the ability to reproduce explicit solvent results, specific software tools have been developed to enable the use of the skin surface in Poisson-Boltzmann calculations with the DelPhi solver. Results indicate that the skin and Connolly surfaces have a comparable performance from this last point of view.
Ringe, Stefan; Oberhofer, Harald; Hille, Christoph; Matera, Sebastian; Reuter, Karsten
2016-08-01
The size-modified Poisson-Boltzmann (MPB) equation is an efficient implicit solvation model which also captures electrolytic solvent effects. It combines an account of the dielectric solvent response with a mean-field description of solvated finite-sized ions. We present a general solution scheme for the MPB equation based on a fast function-space-oriented Newton method and a Green's function preconditioned iterative linear solver. In contrast to popular multigrid solvers, this approach allows us to fully exploit specialized integration grids and optimized integration schemes. We describe a corresponding numerically efficient implementation for the full-potential density-functional theory (DFT) code FHI-aims. We show that together with an additional Stern layer correction the DFT+MPB approach can describe the mean activity coefficient of a KCl aqueous solution over a wide range of concentrations. The high sensitivity of the calculated activity coefficient on the employed ionic parameters thereby suggests to use extensively tabulated experimental activity coefficients of salt solutions for a systematic parametrization protocol.
Cooper, Christopher D
2015-01-01
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 furt...
pKa predictions with a coupled finite difference Poisson-Boltzmann and Debye-Hückel method.
Warwicker, Jim
2011-12-01
Modeling charge interactions is important for understanding many aspects of biological structure and function, and continuum methods such as Finite Difference Poisson-Boltzmann (FDPB) are commonly employed. Calculations of pH-dependence have identified separate populations; surface groups that can be modeled with a simple Debye-Hückel (DH) model, and buried groups, with stronger resultant interactions that are dependent on detailed conformation. This observation led to the development of a combined FDPB and DH method for pK(a) prediction (termed FD/DH). This study reports application of this method to ionizable groups, including engineered buried charges, in staphylococcal nuclease. The data had been made available to interested research groups before publication of mutant structures and/or pK(a) values. Overall, FD/DH calculations perform as intended with low ΔpK(a) values for surface groups (RMSD between predicted and experimental pK(a) values of 0.74), and much larger ΔpK(a) values for the engineered internal groups, with RMSD = 1.64, where mutant structures were known and RMSD = 1.80, where they were modeled. The weaker resultant interactions of the surface groups are determined mostly by charge-charge interactions. For the buried groups, R(2) for correlation between predicted and measured ΔpK(a) values is 0.74, despite the high RMSDs. Charge-charge interactions are much less important, with the R(2) value for buried group ΔpK(a) values increasing to 0.80 when the term describing charge desolvation alone is used. Engineered charge burial delivers a relatively uniform, nonspecific effect, in terms of pK(a) . How the protein environment adapts in atomic detail to deliver this resultant effect is still an open question.
Electro-osmosis of non-Newtonian fluids in porous media using lattice Poisson-Boltzmann method.
Chen, Simeng; He, Xinting; Bertola, Volfango; Wang, Moran
2014-12-15
Electro-osmosis in porous media has many important applications in various areas such as oil and gas exploitation and biomedical detection. Very often, fluids relevant to these applications are non-Newtonian because of the shear-rate dependent viscosity. The purpose of this study was to investigate the behaviors and physical mechanism of electro-osmosis of non-Newtonian fluids in porous media. Model porous microstructures (granular, fibrous, and network) were created by a random generation-growth method. The nonlinear governing equations of electro-kinetic transport for a power-law fluid were solved by the lattice Poisson-Boltzmann method (LPBM). The model results indicate that: (i) the electro-osmosis of non-Newtonian fluids exhibits distinct nonlinear behaviors compared to that of Newtonian fluids; (ii) when the bulk ion concentration or zeta potential is high enough, shear-thinning fluids exhibit higher electro-osmotic permeability, while shear-thickening fluids lead to the higher electro-osmotic permeability for very low bulk ion concentration or zeta potential; (iii) the effect of the porous medium structure depends significantly on the constitutive parameters: for fluids with large constitutive coefficients strongly dependent on the power-law index, the network structure shows the highest electro-osmotic permeability while the granular structure exhibits the lowest permeability on the entire range of power law indices considered; when the dependence of the constitutive coefficient on the power law index is weaker, different behaviors can be observed especially in case of strong shear thinning.
Sun, Hui; Wen, Jiayi; Zhao, Yanxiang; Li, Bo; McCammon, J Andrew
2015-12-28
Dielectric boundary based implicit-solvent models provide efficient descriptions of coarse-grained effects, particularly the electrostatic effect, of aqueous solvent. Recent years have seen the initial success of a new such model, variational implicit-solvent model (VISM) [Dzubiella, Swanson, and McCammon Phys. Rev. Lett. 96, 087802 (2006) and J. Chem. Phys. 124, 084905 (2006)], in capturing multiple dry and wet hydration states, describing the subtle electrostatic effect in hydrophobic interactions, and providing qualitatively good estimates of solvation free energies. Here, we develop a phase-field VISM to the solvation of charged molecules in aqueous solvent to include more flexibility. In this approach, a stable equilibrium molecular system is described by a phase field that takes one constant value in the solute region and a different constant value in the solvent region, and smoothly changes its value on a thin transition layer representing a smeared solute-solvent interface or dielectric boundary. Such a phase field minimizes an effective solvation free-energy functional that consists of the solute-solvent interfacial energy, solute-solvent van der Waals interaction energy, and electrostatic free energy described by the Poisson-Boltzmann theory. We apply our model and methods to the solvation of single ions, two parallel plates, and protein complexes BphC and p53/MDM2 to demonstrate the capability and efficiency of our approach at different levels. With a diffuse dielectric boundary, our new approach can describe the dielectric asymmetry in the solute-solvent interfacial region. Our theory is developed based on rigorous mathematical studies and is also connected to the Lum-Chandler-Weeks theory (1999). We discuss these connections and possible extensions of our theory and methods.
Khoie R.
1996-01-01
Full Text Available A self-consistent Boltzmann-Poisson-Schrödinger solver for High Electron Mobility Transistor is presented. The quantization of electrons in the quantum well normal to the heterojunction is taken into account by solving the two higher moments of Boltzmann equation along with the Schrödinger and Poisson equations, self-consistently. The Boltzmann transport equation in the form of a current continuity equation and an energy balance equation are solved to obtain the transient and steady-state transport behavior. The numerical instability problems associated with the simulator are presented, and the criteria for smooth convergence of the solutions are discussed. The current-voltage characteristics, transconductance, gate capacitance, and unity-gain frequency of a single quantum well HEMT is discussed. It has been found that a HEMT device with a gate length of 0.7 μ m , and with a gate bias voltage of 0.625 V, has a transconductance of 579.2 mS/mm, which together with the gate capacitance of 19.28 pF/cm, can operate at a maximum unity-gain frequency of 47.8 GHz.
R. Khoie
1996-01-01
Full Text Available A self-consistent Boltzmann-Poisson-Schrödinger solver for High Electron Mobility Transistor is presented. The quantization of electrons in the quantum well normal to the heterojunction is taken into account by solving the two higher moments of Boltzmann equation along with the Schrödinger and Poisson equations, self-consistently. The Boltzmann transport equation in the form of a current continuity equation and an energy balance equation are solved to obtain the transient and steady-state transport behavior. The numerical instability problems associated with the simulator are presented, and the criteria for smooth convergence of the solutions are discussed. The current-voltage characteristics, transconductance, gate capacitance, and unity-gain frequency of a single quantum well HEMT is discussed. It has been found that a HEMT device with a gate length of 0.7 μm, and with a gate bias voltage of 0.625 V, has a transconductance of 579.2 mS/mm, which together with the gate capacitance of 19.28 pF/cm, can operate at a maximum unity-gain frequency of 47.8 GHz.
Fogolari, Federico; Corazza, Alessandra; Esposito, Gennaro
2015-04-05
The generalized Born model in the Onufriev, Bashford, and Case (Onufriev et al., Proteins: Struct Funct Genet 2004, 55, 383) implementation has emerged as one of the best compromises between accuracy and speed of computation. For simulations of nucleic acids, however, a number of issues should be addressed: (1) the generalized Born model is based on a linear model and the linearization of the reference Poisson-Boltmann equation may be questioned for highly charged systems as nucleic acids; (2) although much attention has been given to potentials, solvation forces could be much less sensitive to linearization than the potentials; and (3) the accuracy of the Onufriev-Bashford-Case (OBC) model for nucleic acids depends on fine tuning of parameters. Here, we show that the linearization of the Poisson Boltzmann equation has mild effects on computed forces, and that with optimal choice of the OBC model parameters, solvation forces, essential for molecular dynamics simulations, agree well with those computed using the reference Poisson-Boltzmann model. © 2015 Wiley Periodicals, Inc.
Carrillo, J A; Majorana, A; Shu, C W
2003-01-01
In this paper we develop a deterministic high order accurate finite-difference WENO solver to the solution of the 1-D Boltzmann-Poisson system for semiconductor devices. We follow the work in Fatemi and Odeh and in Majorana and Pidatella to formulate the Boltzmann-Poisson system in a spherical coordinate system using the energy as one of the coordinate variables, thus reducing the computational complexity to two dimensions in phase space and dramatically simplifying the evaluations of the collision terms. The solver is accurate in time hence potentially useful for time-dependent simulations, although in this paper we only test it for steady-state devices. The high order accuracy and nonoscillatory properties of the solver allow us to use very coarse meshes to get a satisfactory resolution, thus making it feasible to develop a 2-D solver (which will be five dimensional plus time when the phase space is discretized) on today's computers. The computational results have been compared with those by a Monte Carlo s...
Free Surface Lattice Boltzmann with Enhanced Bubble Model
Anderl, Daniela; Rauh, Cornelia; Rüde, Ulrich; Delgado, Antonio
2016-01-01
This paper presents an enhancement to the free surface lattice Boltzmann method (FSLBM) for the simulation of bubbly flows including rupture and breakup of bubbles. The FSLBM uses a volume of fluid approach to reduce the problem of a liquid-gas two-phase flow to a single-phase free surface simulation. In bubbly flows compression effects leading to an increase or decrease of pressure in the suspended bubbles cannot be neglected. Therefore, the free surface simulation is augmented by a bubble model that supplies the missing information by tracking the topological changes of the free surface in the flow. The new model presented here is capable of handling the effects of bubble breakup and coalesce without causing a significant computational overhead. Thus, the enhanced bubble model extends the applicability of the FSLBM to a new range of practically relevant problems, like bubble formation and development in chemical reactors or foaming processes.
舒英; 章顺; 吴文青; 黄自萍
2002-01-01
本文对分子生物物理学中产生的线性Poisson-Boltzmann方程(PBE),给出了Mortar有限元方法的计算过程,数值计算例子表明,与一般的协调有限元方法相比,用Mortar元方法求解此类有间断系数的问题是非常有效的.
崔国忠; 张志平; 江成顺
2002-01-01
This paper deals with the initial boundary value problem for the BoltzmannPoisson system, which arises in semiconductor physics, with absorbing boundary. The global existence of weak solutions is proved by using the stability of velocity averages and the compactness results on L1-theory under weaker conditons on initial boundary values.
Thereza A. Soares
2004-08-01
Full Text Available The ability of biomolecules to catalyze chemical reactions is due chiefly to their sensitivity to variations of the pH in the surrounding environment. The reason for this is that they are made up of chemical groups whose ionization states are modulated by pH changes that are of the order of 0.4 units. The determination of the protonation states of such chemical groups as a function of conformation of the biomolecule and the pH of the environment can be useful in the elucidation of important biological processes from enzymatic catalysis to protein folding and molecular recognition. In the past 15 years, the theory of Poisson-Boltzmann has been successfully used to estimate the pKa of ionizable sites in proteins yielding results, which may differ by 0.1 unit from the experimental values. In this study, we review the theory of Poisson-Boltzmann under the perspective of its application to the calculation of pKa in proteins.
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
Teixeira, Vitor H; Cunha, Carlos A; Machuqueiro, Miguel; Oliveira, A Sofia F; Victor, Bruno L; Soares, Cláudio M; Baptista, António M
2005-08-04
Poisson-Boltzmann (PB) models are a fast and common tool for studying electrostatic processes in proteins, particularly their ionization equilibrium (protonation and/or reduction), often yielding quite good results when compared with more detailed models. Yet, they are conceptually very simple and necessarily approximate, their empirical character being most evident when it comes to the choice of the dielectric constant assigned to the protein region. The present study analyzes several factors affecting the ability of PB-based methods to model protein ionization equilibrium. We give particular attention to a suggestion made by Warshel and co-workers (e.g., Sham et al. J. Phys. Chem. B 1997, 101, 4458) of using different protein dielectric constants for computing the individual (site) and the pairwise (site-site) terms of the ionization free energies. Our prediction of pK(a) values for several proteins indicates that no advantage is obtained by such a procedure, even for sites that are buried and/or display large pK(a) shifts relative to the solution values. In particular, the present methodology gives the best predictions using a dielectric constant around 20, for shifted/buried and nonshifted/exposed sites alike. The similarities and differences between the PB model and Warshel's PDLD/S model are discussed, as well as the reasons behind their apparently discrepant results. The present PB model is shown to predict also good reduction potentials in redox proteins.
Bredenberg, Johan H; Russo, Cristina; Fenley, Marcia O
2008-06-01
The TATA-binding protein (TBP) is a key component of the archaea ternary preinitiation transcription assembly. The archaeon TBP, from the halophile/hyperthermophile organism Pyrococcus woesei, is adapted to high concentrations of salt and high-temperature environments. Although most eukaryotic TBPs are mesophilic and adapted to physiological conditions of temperature and salt, they are very similar to their halophilic counterparts in sequence and fold. However, whereas the binding affinity to DNA of halophilic TBPs increases with increasing salt concentration, the opposite is observed for mesophilic TBPs. We investigated these differences in nonspecific salt-dependent DNA-binding behavior of halophilic and mesophilic TBPs by using a combined molecular mechanics/Poisson-Boltzmann approach. Our results are qualitatively in good agreement with experimentally observed salt-dependent DNA-binding for mesophilic and halophilic TBPs, and suggest that the distribution and the total number of charged residues may be the main underlying contributor in the association process. Therefore, the difference in the salt-dependent binding behavior of mesophilic and halophilic TBPs to DNA may be due to the very unique charge and electrostatic potential distribution of these TBPs, which consequently alters the number of repulsive and attractive electrostatic interactions.
Biesheuvel, PM; van der Veen, M; Norde, W
2005-01-01
The equilibrium adsorption of polyelectrolytes with multiple types of ionizable groups is described using a modified Poisson-Boltzrnann equation including charge regulation of both the polymer and the interface. A one-dimensional mean-field model is used in which the electrostatic potential is
Enhancement of the stability of lattice Boltzmann methods by dissipation control
Gorban, A. N.; Packwood, D. J.
2014-11-01
Artificial dissipation is a well known tool for the improvement of stability of numerical algorithms. However, the use of this technique affects the accuracy of the computation. We analyse various approaches proposed for enhancement of the Lattice Boltzmann Methods’ (LBM) stability. In addition to some previously known methods, the Multiple Relaxation Time (MRT) models, the entropic lattice Boltzmann method (ELBM), and filtering (including entropic median filtering), we develop and analyse new filtering techniques with independent filtering of different modes. All these methods affect dissipation in the system and may adversely affect the reproduction of the proper physics. To analyse the effect of dissipation on accuracy and to prepare practical recommendations, we test the enhanced LBM methods on the standard benchmark, the 2D lid driven cavity on a coarse grid (101×101 nodes). The accuracy was estimated by the position of the first Hopf bifurcation points in these systems. We find that two techniques, MRT and median filtering, succeed in yielding a reasonable value of the Reynolds number for the first bifurcation point. The newly created limiters, which filter the modes independently, also pick a reasonable value of the Reynolds number for the first bifurcation.
Sugimoto, Yu; Kitazumi, Yuki; Shirai, Osamu; Yamamoto, Masahiro; Kano, Kenji
2016-03-31
To understand electrostatic interactions in biomolecules, the bimolecular rate constants (k) between redox enzymes and charged substrates (in this study, redox mediators in the electrode reaction) were evaluated at various ionic strengths (I) for the mediated bioelectrocatalytic reaction. The k value between bilirubin oxidase (BOD) and positively charged mediators increased with I, while that between BOD and negatively charged mediators decreased with I. The opposite trend was observed for the reaction of glucose oxidase (GOD). In the case of noncharged mediators, the k value was independent of I for both BOD and GOD. These results reflect the electrostatic interactions between the enzymes and the mediators. Furthermore, we estimated k/k° (k° being the thermodynamic rate constant) by numerical simulation (finite element method) based on the Poisson-Boltzmann (PB) equation. By considering the charges of individual atoms involved in the amino acids around the substrate binding sites in the enzymes, the simulated k/k° values well reproduced the experimental data. In conclusion, k/k° can be predicted by PB-based simulation as long as the crystal structure of the enzyme and the substrate binding site are known.
Savita Agrawal
2015-11-01
Full Text Available In the last decades, image segmentation has proved its applicability in various areas like satellite image processing, medical image processing and many more. In the present scenario the researchers tries to develop hybrid image segmentation techniques to generates efficient segmentation. Due to the development of the parallel programming, the lattice Boltzmann method (LBM has attracted much attention as a fast alternative approach for solving partial differential equations. In this project work, first designed an energy functional based on the fuzzy c-means objective function which incorporates the bias field that accounts for the intensity in homogeneity of the real-world image. Using the gradient descent method, corresponding level set equations are obtained from which we deduce a fuzzy external force for the LBM solver based on the model by Zhao. The method is speedy, robust for denoise, and does not dependent on the position of the initial contour, effective in the presence of intensity in homogeneity, highly parallelizable and can detect objects with or without edges. For the implementation of segmentation techniques defined for gray images, most of the time researchers determines single channel segments of the images and superimposes the single channel segment information on color images. This idea leads to provide color image segmentation using single channel segments of multi channel images. Though this method is widely adopted but doesn’t provide complete true segmentation of multichannel ie color images because a color image contains three different channels for Red, green and blue components. Hence segmenting a color image, by having only single channel segments information, will definitely loose important segment regions of color images. To overcome this problem this paper work starts with the development of Enhanced Level Set Segmentation for single channel Images Using Fuzzy Clustering and Lattice Boltzmann Method. For the
Savita Agrawal
2014-05-01
Full Text Available In the last decades, image segmentation has proved its applicability in various areas like satellite image processing, medical image processing and many more. In the present scenario the researchers tries to develop hybrid image segmentation techniques to generates efficient segmentation. Due to the development of the parallel programming, the lattice Boltzmann met hod (LBM has attracted much attention as a fast alternative approach for solving partial differential equations. In this project work, first designed an energy functional based on the fuzzy c-means objective function which incorporates the bias field that accounts for the intensity in homogeneity of the real-world image. Using the gradient descent method, corresponding level set equations are obtained from which we deduce a fuzzy external force for the LBM solver based on the model by Zhao. The method is speedy, robust for denoise, and does not dependent on the position of the initial contour, effective in the presence of intensity in homogeneity, highly parallelizable and can detect objects with or without edges. For the implementation of segmentation techniques defined for gr ay images, most of the time researchers determines single channel segments of the images and superimposes the single channel segment information on color images. This idea leads to provide color image segmentation using single channel segments of multi chann el images. Though this method is widely adopted but doesn’t provide complete true segmentation of multichannel ie color images because a color image contains three different channels for Red, green and blue components. Hence segmenting a color image, b y having only single channel segments information, will definitely loose important segment regions of color images. To overcome this problem this paper work starts with the development of Enhanced Level Set Segmentation for single channel Images Using Fuzzy Clustering and Lattice Boltzmann Method. For the
Gavryushov, Sergei
2007-05-17
Potentials of mean force between single Na+, Ca2+, and Mg2+ cations and a highly charged spherical macroion in SPC/E water have been determined using molecular dynamics simulations. Results are compared to the electrostatic energy calculations for the primitive polarization model (PPM) of hydrated cations describing the ion hydration shell as a dielectric sphere of low permittivity (Gavryushov, S.; Linse, P. J. Phys. Chem. B 2003, 107, 7135). Parameters of the ion dielectric sphere and radius of the macroion/water dielectric boundary were extracted by means of this comparison to approximate the short-range repulsion of ions near the interface. To explore the counterion distributions around a simplified model of DNA, the obtained PPM parameters for Na+ and Ca2+ have been substituted into the modified Poisson-Boltzmann (MPB) equations derived for the PPM and named the epsilon-MPB (epsilon-MPB) theory. epsilon-MPB results for DNA suggest that such polarization effects are important in the case of 2:1 electrolyte and highly charged macromolecules. The three-dimensional implementation of the epsilon-MPB theory was also applied to calculation of the energies of interaction between two parallel macromolecules of DNA in solutions of NaCl and CaCl2. Being compared to results of MPB calculations without the ion polarization effects, it suggests that the ion hydration shell polarization and inhomogeneous solvent permittivity might be essential factors in the experimentally known hydration forces acting between charged macromolecules and bilayers at separations of less than 20 A between their surfaces.
Fokianos, Konstantinos; Rahbek, Anders Christian; Tjøstheim, Dag
This paper considers geometric ergodicity and likelihood based inference for linear and nonlinear Poisson autoregressions. In the linear case the conditional mean is linked linearly to its past values as well as the observed values of the Poisson process. This also applies to the conditional...
Fokianos, Konstantinos; Rahbek, Anders Christian; Tjøstheim, Dag
This paper considers geometric ergodicity and likelihood based inference for linear and nonlinear Poisson autoregressions. In the linear case the conditional mean is linked linearly to its past values as well as the observed values of the Poisson process. This also applies to the conditional...... variance, implying an interpretation as an integer valued GARCH process. In a nonlinear conditional Poisson model, the conditional mean is a nonlinear function of its past values and a nonlinear function of past observations. As a particular example an exponential autoregressive Poisson model for time...... series is considered. Under geometric ergodicity the maximum likelihood estimators of the parameters are shown to be asymptotically Gaussian in the linear model. In addition we provide a consistent estimator of the asymptotic covariance, which is used in the simulations and the analysis of some...
Fokianos, Konstantinos; Rahbek, Anders Christian; Tjøstheim, Dag
2009-01-01
In this article we consider geometric ergodicity and likelihood-based inference for linear and nonlinear Poisson autoregression. In the linear case, the conditional mean is linked linearly to its past values, as well as to the observed values of the Poisson process. This also applies...... to the conditional variance, making possible interpretation as an integer-valued generalized autoregressive conditional heteroscedasticity process. In a nonlinear conditional Poisson model, the conditional mean is a nonlinear function of its past values and past observations. As a particular example, we consider...... an exponential autoregressive Poisson model for time series. Under geometric ergodicity, the maximum likelihood estimators are shown to be asymptotically Gaussian in the linear model. In addition, we provide a consistent estimator of their asymptotic covariance matrix. Our approach to verifying geometric...
Fokianos, Konstantinos; Rahbæk, Anders; Tjøstheim, Dag
This paper considers geometric ergodicity and likelihood based inference for linear and nonlinear Poisson autoregressions. In the linear case the conditional mean is linked linearly to its past values as well as the observed values of the Poisson process. This also applies to the conditional...... variance, making an interpretation as an integer valued GARCH process possible. In a nonlinear conditional Poisson model, the conditional mean is a nonlinear function of its past values and a nonlinear function of past observations. As a particular example an exponential autoregressive Poisson model...... for time series is considered. Under geometric ergodicity the maximum likelihood estimators of the parameters are shown to be asymptotically Gaussian in the linear model. In addition we provide a consistent estimator of their asymptotic covariance matrix. Our approach to verifying geometric ergodicity...
Li, Xian-Ying; Hu, Shi-Min
2013-02-01
Harmonic functions are the critical points of a Dirichlet energy functional, the linear projections of conformal maps. They play an important role in computer graphics, particularly for gradient-domain image processing and shape-preserving geometric computation. We propose Poisson coordinates, a novel transfinite interpolation scheme based on the Poisson integral formula, as a rapid way to estimate a harmonic function on a certain domain with desired boundary values. Poisson coordinates are an extension of the Mean Value coordinates (MVCs) which inherit their linear precision, smoothness, and kernel positivity. We give explicit formulas for Poisson coordinates in both continuous and 2D discrete forms. Superior to MVCs, Poisson coordinates are proved to be pseudoharmonic (i.e., they reproduce harmonic functions on n-dimensional balls). Our experimental results show that Poisson coordinates have lower Dirichlet energies than MVCs on a number of typical 2D domains (particularly convex domains). As well as presenting a formula, our approach provides useful insights for further studies on coordinates-based interpolation and fast estimation of harmonic functions.
Enhanced Night Vision Via a Combination of Poisson Interpolation and Machine Learning
2006-02-01
21(4), 291-310. RASKAR, R., ILIE, A., and YU, J. 2004. Image Fusion for Context Enhancement and Video Surrealism . In Proceedings of the...chosen in a pop -up dialog. - HDR : Build Dark HDR Unsupported - HDR : 10-50-500 Unsupported - HDR : Gamma Correct Applies a 1/gamma global
Lattice Boltzmann model for nanofluids
Xuan Yimin; Yao Zhengping [Nanjing University of Science and Technology, School of Power Engineering, Nanjing (China)
2005-01-01
A nanofluid is a particle suspension that consists of base liquids and nanoparticles and has great potential for heat transfer enhancement. By accounting for the external and internal forces acting on the suspended nanoparticles and interactions among the nanoparticles and fluid particles, a lattice Boltzmann model is proposed for simulating flow and energy transport processes inside the nanofluids. First, we briefly introduce the conventional lattice Boltzmann model for multicomponent systems. Then, we discuss the irregular motion of the nanoparticles and inherent dynamic behavior of nanofluids and describe a lattice Boltzmann model for simulating nanofluids. Finally, we conduct some calculations for the distribution of the suspended nanoparticles. (orig.)
Boltzmann-Electron Model in Aleph.
Hughes, Thomas Patrick; Hooper, Russell
2014-11-01
We apply the Boltzmann-electron model in the electrostatic, particle-in-cell, finite- element code Aleph to a plasma sheath. By assuming a Boltzmann energy distribution for the electrons, the model eliminates the need to resolve the electron plasma fre- quency, and avoids the numerical "grid instability" that can cause unphysical heating of electrons. This allows much larger timesteps to be used than with kinetic electrons. Ions are treated with the standard PIC algorithm. The Boltzmann-electron model re- quires solution of a nonlinear Poisson equation, for which we use an iterative Newton solver (NOX) from the Trilinos Project. Results for the spatial variation of density and voltage in the plasma sheath agree well with an analytic model
Felluga, Alessandro
2011-01-01
A new distribution called natural distribution is introduced with the intent of merging statistics and empirical data. Based on the probability derived from the Bernoulli distribution, this method extended also Poisson distribution to continuous, preserving its skewness. Using this model, the Horwitz curve has been explained. The theoretical derivation of our method, which applies to every kind of measurements collected through sampling, is here supported by a mathematical demonstration and illustrated with several applications to real data collected from chemical and geotechnical fields. We compared the proposed natural distribution to other widely-used frequency functions to test the robustness of the proposed method in fitting the histograms and the probability charts obtained from various intensive variables.
Central simple Poisson algebras
SU Yucai; XU Xiaoping
2004-01-01
Poisson algebras are fundamental algebraic structures in physics and symplectic geometry. However, the structure theory of Poisson algebras has not been well developed. In this paper, we determine the structure of the central simple Poisson algebras related to locally finite derivations, over an algebraically closed field of characteristic zero.The Lie algebra structures of these Poisson algebras are in general not finitely-graded.
Poisson Morphisms and Reduced Affine Poisson Group Actions
YANG Qi Lin
2002-01-01
We establish the concept of a quotient affine Poisson group, and study the reduced Poisson action of the quotient of an affine Poisson group G on the quotient of an affine Poisson G-variety V. The Poisson morphisms (including equivariant cases) between Poisson affine varieties are also discussed.
Progress in developing Poisson-Boltzmann equation solvers
Li, Chuan; Li, Lin; Petukh, Marharyta; Alexov, Emil
2013-01-01
This review outlines the recent progress made in developing more accurate and efficient solutions to model electrostatics in systems comprised of bio-macromolecules and nano-objects, the last one referring to objects that do not have biological function themselves but nowadays are frequently used in biophysical and medical approaches in conjunction with bio-macromolecules. The problem of modeling macromolecular electrostatics is reviewed from two different angles: as a mathematical task provided the specific definition of the system to be modeled and as a physical problem aiming to better capture the phenomena occurring in the real experiments. In addition, specific attention is paid to methods to extend the capabilities of the existing solvers to model large systems toward applications of calculations of the electrostatic potential and energies in molecular motors, mitochondria complex, photosynthetic machinery and systems involving large nano-objects. PMID:24199185
Progress in developing Poisson-Boltzmann equation solvers.
Li, Chuan; Li, Lin; Petukh, Marharyta; Alexov, Emil
2013-03-01
This review outlines the recent progress made in developing more accurate and efficient solutions to model electrostatics in systems comprised of bio-macromolecules and nano-objects, the last one referring to objects that do not have biological function themselves but nowadays are frequently used in biophysical and medical approaches in conjunction with bio-macromolecules. The problem of modeling macromolecular electrostatics is reviewed from two different angles: as a mathematical task provided the specific definition of the system to be modeled and as a physical problem aiming to better capture the phenomena occurring in the real experiments. In addition, specific attention is paid to methods to extend the capabilities of the existing solvers to model large systems toward applications of calculations of the electrostatic potential and energies in molecular motors, mitochondria complex, photosynthetic machinery and systems involving large nano-objects.
Suzuki, Hideyuki; Imura, Jun-ichi; Horio, Yoshihiko; Aihara, Kazuyuki
2013-01-01
The chaotic Boltzmann machine proposed in this paper is a chaotic pseudo-billiard system that works as a Boltzmann machine. Chaotic Boltzmann machines are shown numerically to have computing abilities comparable to conventional (stochastic) Boltzmann machines. Since no randomness is required, efficient hardware implementation is expected. Moreover, the ferromagnetic phase transition of the Ising model is shown to be characterised by the largest Lyapunov exponent of the proposed system. In general, a method to relate probabilistic models to nonlinear dynamics by derandomising Gibbs sampling is presented.
Sman, van der R.G.M.
2006-01-01
In the special case of relaxation parameter = 1 lattice Boltzmann schemes for (convection) diffusion and fluid flow are equivalent to finite difference/volume (FD) schemes, and are thus coined finite Boltzmann (FB) schemes. We show that the equivalence is inherent to the homology of the
Alizadeh, A; Wang, J K; Pooyan, S; Mirbozorgi, S A; Wang, M
2013-10-01
In this paper, the effect of temperature difference between inlet flow and walls on the electro-osmotic flow through a two-dimensional microchannel is investigated. The main objective is to study the effect of temperature variations on the distribution of ions and consequently internal electric potential field, electric body force, and velocity fields in an electro-osmotic flow. We assume constant temperature and zeta potential on walls and use the mean temperature of each cross section to characterize the Boltzmann ion distribution across the channel. Based on these assumptions, the multiphysical transports are still able to be described by the classical Poisson-Boltzmann model. In this work, the Navier-Stokes equation for fluid flow, the Poisson-Boltzmann equation for ion distribution, and the energy equation for heat transfer are solved by a couple lattice Boltzmann method. The modeling results indicate that the temperature difference between walls and the inlet solution may lead to two symmetrical vortices at the entrance region of the microchannel which is appropriate for mixing enhancements. The advantage of this phenomenon for active control of mixing in electro-osmotic flow is the manageability of the vortex scale without extra efforts. For instance, the effective domain of this pattern could broaden by the following modulations: decreasing the external electric potential field, decreasing the electric double layer thickness, or increasing the temperature difference between inlet flow and walls. This work may provide a novel strategy for design or optimization of microsystems. Copyright © 2013 Elsevier Inc. All rights reserved.
Extended Poisson Exponential Distribution
Anum Fatima
2015-09-01
Full Text Available A new mixture of Modified Exponential (ME and Poisson distribution has been introduced in this paper. Taking the Maximum of Modified Exponential random variable when the sample size follows a zero truncated Poisson distribution we have derived the new distribution, named as Extended Poisson Exponential distribution. This distribution possesses increasing and decreasing failure rates. The Poisson-Exponential, Modified Exponential and Exponential distributions are special cases of this distribution. We have also investigated some mathematical properties of the distribution along with Information entropies and Order statistics of the distribution. The estimation of parameters has been obtained using the Maximum Likelihood Estimation procedure. Finally we have illustrated a real data application of our distribution.
Johnson, D H
2009-01-01
What constitutes jointly Poisson processes remains an unresolved issue. This report reviews the current state of the theory and indicates how the accepted but unproven model equals that resulting from the small time-interval limit of jointly Bernoulli processes. One intriguing consequence of these models is that jointly Poisson processes can only be positively correlated as measured by the correlation coefficient defined by cumulants of the probability generating functional.
Negative Poisson's Ratio in Modern Functional Materials.
Huang, Chuanwei; Chen, Lang
2016-10-01
Materials with negative Poisson's ratio attract considerable attention due to their underlying intriguing physical properties and numerous promising applications, particularly in stringent environments such as aerospace and defense areas, because of their unconventional mechanical enhancements. Recent progress in materials with a negative Poisson's ratio are reviewed here, with the current state of research regarding both theory and experiment. The inter-relationship between the underlying structure and a negative Poisson's ratio is discussed in functional materials, including macroscopic bulk, low-dimensional nanoscale particles, films, sheets, or tubes. The coexistence and correlations with other negative indexes (such as negative compressibility and negative thermal expansion) are also addressed. Finally, open questions and future research opportunities are proposed for functional materials with negative Poisson's ratios.
Ludwig Boltzmann: Atomic genius
Cercignani, C. [Department of Mathematics, Politecnico di Milano (Italy)]. E-mail: carcer@mate.polimi.it
2006-09-15
On the centenary of the death of Ludwig Boltzmann, Carlo Cercignani examines the immense contributions of the man who pioneered our understanding of the atomic nature of matter. The man who first gave a convincing explanation of the irreversibility of the macroscopic world and the symmetry of the laws of physics was the Austrian physicist Ludwig Boltzmann, who tragically committed suicide 100 years ago this month. One of the key figures in the development of the atomic theory of matter, Boltzmann's fame will be forever linked to two fundamental contributions to science. The first was his interpretation of 'entropy' as a mathematically well-defined measure of the disorder of atoms. The second was his derivation of what is now known as the Boltzmann equation, which describes the statistical properties of a gas as made up of molecules. The equation, which described for the first time how a probability can evolve with time, allowed Boltzmann to explain why macroscopic phenomena are irreversible. The key point is that while microscopic objects like atoms can behave reversibly, we never see broken coffee cups reforming because it would involve a long series of highly improbable interactions - and not because it is forbidden by the laws of physics. (U.K.)
Generalized Poisson sigma models
Batalin, I; Batalin, Igor; Marnelius, Robert
2001-01-01
A general master action in terms of superfields is given which generates generalized Poisson sigma models by means of a natural ghost number prescription. The simplest representation is the sigma model considered by Cattaneo and Felder. For Dirac brackets considerably more general models are generated.
Matsuo, Kuniaki; Saleh, Bahaa E. A.; Teich, Malvin Carl
1982-12-01
We investigate the counting statistics for stationary and nonstationary cascaded Poisson processes. A simple equation is obtained for the variance-to-mean ratio in the limit of long counting times. Explicit expressions for the forward-recurrence and inter-event-time probability density functions are also obtained. The results are expected to be of use in a number of areas of physics.
Poisson Random Variate Generation.
1981-12-01
Poisson have been proposed. Atkinson [5] includes the approach developed in Marsaglia £15) and Norman and Cannon £16) which is based on composition...34, Naval Research Logistics Quarterly, 26, 3, 403-413. 15. Marsaglia , G. (1963). "Generating Discrete Random Variables in a Computer", Communications
THE NON-CUTOFF BOLTZMANN EQUATION WITH POTENTIAL FORCE IN THE WHOLE SPACE
Yuanjie LEI
2014-01-01
This paper is concerned with the non-cutoff Boltzmann equation for full-range interactions with potential force in the whole space. We establish the global existence and optimal temporal convergence rates of classical solutions to the Cauchy problem when initial data is a small perturbation of the stationary solution. The analysis is based on the time-weighted energy method building also upon the recent studies of the non-cutoff Boltzmann equation in [1-3, 15] and the non-cutoff Vlasov-Poisson-Boltzmann system [6].
Lattice Boltzmann Stokesian dynamics.
Ding, E J
2015-11-01
Lattice Boltzmann Stokesian dynamics (LBSD) is presented for simulation of particle suspension in Stokes flows. This method is developed from Stokesian dynamics (SD) with resistance and mobility matrices calculated using the time-independent lattice Boltzmann algorithm (TILBA). TILBA is distinguished from the traditional lattice Boltzmann method (LBM) in that a background matrix is generated prior to the calculation. The background matrix, once generated, can be reused for calculations for different scenarios, thus the computational cost for each such subsequent calculation is significantly reduced. The LBSD inherits the merits of the SD where both near- and far-field interactions are considered. It also inherits the merits of the LBM that the computational cost is almost independent of the particle shape.
Lindley, David
2002-01-01
Ludwig Boltzmann (1844-1906) è il fisico e matematico austriaco che negli ultimi decenni dell'Ottocento e ancora ai primi del Novecento lottò contro l'opinione dominante tra gli scienziati dell'epoca per affermare la teoria atomica della materia. È noto come con Albert Einstein e fino a oggi la fisica si sia sviluppata e abbia celebrato i propri trionfi lungo le linee anticipate da Boltzmann. La controversia con Mach non riguardava soltanto l'esistenza degli atomi, ma l'intero modo di fare fisica che Boltzmann non riteneva di dover limitare allo studio di quantità misurabili, introducendo invece spiegazioni più elaborate basate su ipotesi più ampie.
崔国忠; 张志平; 等
2002-01-01
This paper deals with the initial boundary value value problem for the Boltzmann-Poisson system ,which arises in semiconductor physics,with absorbing boundary.The global existence of weak solutions is proved by using the stability of velocity averages and the compactness results on L1-theory under weaker conditons on initial boundary values.
Formal equivalence of Poisson structures around Poisson submanifolds
Marcut, I.T.
2012-01-01
Let (M,π) be a Poisson manifold. A Poisson submanifold P ⊂ M gives rise to a Lie algebroid AP → P. Formal deformations of π around P are controlled by certain cohomology groups associated to AP. Assuming that these groups vanish, we prove that π is formally rigid around P; that is, any other Poisson
High-Order Kinetic Relaxation Schemes as High-Accuracy Poisson Solvers
Mendoza, M; Herrmann, H J
2015-01-01
We present a new approach to find accurate solutions to the Poisson equation, as obtained from the steady-state limit of a diffusion equation with strong source terms. For this purpose, we start from Boltzmann's kinetic theory and investigate the influence of higher order terms on the resulting macroscopic equations. By performing an appropriate expansion of the equilibrium distribution, we provide a method to remove the unnecessary terms up to a desired order and show that it is possible to find, with high level of accuracy, the steady-state solution of the diffusion equation for sizeable Knudsen numbers. In order to test our kinetic approach, we discretise the Boltzmann equation and solve the Poisson equation, spending up to six order of magnitude less computational time for a given precision than standard lattice Boltzmann methods.
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.
Training Restricted Boltzmann Machines
Fischer, Asja
Restricted Boltzmann machines (RBMs) are probabilistic graphical models that can also be interpreted as stochastic neural networks. Training RBMs is known to be challenging. Computing the likelihood of the model parameters or its gradient is in general computationally intensive. Thus, training...
SYMPLECTIC STRUCTURE OF POISSON SYSTEM
SUN Jian-qiang; MA Zhong-qi; TIAN Yi-min; QIN Meng-zhao
2005-01-01
When the Poisson matrix of Poisson system is non-constant, classical symplectic methods, such as symplectic Runge-Kutta method, generating function method, cannot preserve the Poisson structure. The non-constant Poisson structure was transformed into the symplectic structure by the nonlinear transform.Arbitrary order symplectic method was applied to the transformed Poisson system. The Euler equation of the free rigid body problem was transformed into the symplectic structure and computed by the mid-point scheme. Numerical results show the effectiveness of the nonlinear transform.
Reprint of : The Boltzmann--Langevin approach: A simple quantum-mechanical derivation
Nagaev, K. E.
2016-08-01
We present a simple quantum-mechanical derivation of correlation function of Langevin sources in the semiclassical Boltzmann-Langevin equation. The specific case of electron-phonon scattering is considered. It is shown that the assumption of weak scattering leads to the Poisson nature of the scattering fluxes.
Parametric lattice Boltzmann method
Shim, Jae Wan
2017-06-01
The discretized equilibrium distributions of the lattice Boltzmann method are presented by using the coefficients of the Lagrange interpolating polynomials that pass through the points related to discrete velocities and using moments of the Maxwell-Boltzmann distribution. The ranges of flow velocity and temperature providing positive valued distributions vary with regulating discrete velocities as parameters. New isothermal and thermal compressible models are proposed for flows of the level of the isothermal and thermal compressible Navier-Stokes equations. Thermal compressible shock tube flows are simulated by only five on-lattice discrete velocities. Two-dimensional isothermal and thermal vortices provoked by the Kelvin-Helmholtz instability are simulated by the parametric models.
Poisson modules and degeneracy loci
Gualtieri, Marco
2012-01-01
In this paper, we study the interplay between modules and sub-objects in holomorphic Poisson geometry. In particular, we define a new notion of "residue" for a Poisson module, analogous to the Poincar\\'e residue of a meromorphic volume form. Of particular interest is the interaction between the residues of the canonical line bundle of a Poisson manifold and its degeneracy loci---where the rank of the Poisson structure drops. As an application, we provide new evidence in favour of Bondal's conjecture that the rank \\leq 2k locus of a Fano Poisson manifold always has dimension \\geq 2k+1. In particular, we show that the conjecture holds for Fano fourfolds. We also apply our techniques to a family of Poisson structures defined by Fe\\u{\\i}gin and Odesski\\u{\\i}, where the degeneracy loci are given by the secant varieties of elliptic normal curves.
Fiorentino, Eve-Agnès; Toussaint, Renaud; Jouniaux, Laurence
2017-02-01
The streaming potential phenomenon is an electrokinetic effect that occurs in porous media. It is characterized by an electrokinetic (EK) coefficient. The aim of this paper is to simulate the EK coefficient in unsaturated conditions using the Lattice Boltzmann method in a 2-D capillary channel. The multiphase flow is simulated with the model of Shan & Chen. The Poisson-Boltzmann equation is solved by implementing the model of Chai & Shi. The streaming potential response shows a non-monotonous behaviour due to the combination of the increase of charge density and decrease of flow velocity with decreasing water saturation. Using a ζ potential of -20 mV at the air-water interface, an enhancement of a factor 5-30 of the EK coefficient, compared to the saturated state, can be observed due to the positive charge excess at this interface which is magnified by the fluid velocity away from the rock surface. This enhancement is correlated to the fractioning of the bubbles, and to the dynamic state of these bubbles, moving or entrapped in the crevices of the channel.
Eliazar, Iddo; Klafter, Joseph
2008-09-01
The Central Limit Theorem (CLT) and Extreme Value Theory (EVT) study, respectively, the stochastic limit-laws of sums and maxima of sequences of independent and identically distributed (i.i.d.) random variables via an affine scaling scheme. In this research we study the stochastic limit-laws of populations of i.i.d. random variables via nonlinear scaling schemes. The stochastic population-limits obtained are fractal Poisson processes which are statistically self-similar with respect to the scaling scheme applied, and which are characterized by two elemental structures: (i) a universal power-law structure common to all limits, and independent of the scaling scheme applied; (ii) a specific structure contingent on the scaling scheme applied. The sum-projection and the maximum-projection of the population-limits obtained are generalizations of the classic CLT and EVT results - extending them from affine to general nonlinear scaling schemes.
Nonhomogeneous fractional Poisson processes
Wang Xiaotian [School of Management, Tianjin University, Tianjin 300072 (China)]. E-mail: swa001@126.com; Zhang Shiying [School of Management, Tianjin University, Tianjin 300072 (China); Fan Shen [Computer and Information School, Zhejiang Wanli University, Ningbo 315100 (China)
2007-01-15
In this paper, we propose a class of non-Gaussian stationary increment processes, named nonhomogeneous fractional Poisson processes W{sub H}{sup (j)}(t), which permit the study of the effects of long-range dependance in a large number of fields including quantum physics and finance. The processes W{sub H}{sup (j)}(t) are self-similar in a wide sense, exhibit more fatter tail than Gaussian processes, and converge to the Gaussian processes in distribution in some cases. In addition, we also show that the intensity function {lambda}(t) strongly influences the existence of the highest finite moment of W{sub H}{sup (j)}(t) and the behaviour of the tail probability of W{sub H}{sup (j)}(t)
Analysis of Jeans instability from the Boltzmann equation
Kremer, Gilberto M.
2016-11-01
The dynamics of self-gravitating fluids is analyzed within the framework of a collisionless Boltzmann equation in the presence of gravitational fields and Poisson equation. Two cases are analyzed: a system with baryonic and dark matter in a static universe and a single system in an expanding universe. The amplitudes of the perturbed distribution functions are considered as a linear combination of the collision invariants of the Boltzmann equation. For the system of baryonic and dark matter, the Jeans mass of the combined system is smaller than the one of the single system indicating that a smaller mass is needed to initiate the collapse. For the single system in an expanding universe it is not necessary to make use of Jeans "swindle"and it shown that for small wavelengths the density contrast oscillates while for large wavelengths it grows with time and the Jeans instability emerges.
Poisson Spot with Magnetic Levitation
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.
Poisson hierarchy of discrete strings
Ioannidou, Theodora, E-mail: ti3@auth.gr [Faculty of Civil Engineering, School of Engineering, Aristotle University of Thessaloniki, 54249, Thessaloniki (Greece); Niemi, Antti J., E-mail: Antti.Niemi@physics.uu.se [Department of Physics and Astronomy, Uppsala University, P.O. Box 803, S-75108, Uppsala (Sweden); Laboratoire de Mathematiques et Physique Theorique CNRS UMR 6083, Fédération Denis Poisson, Université de Tours, Parc de Grandmont, F37200, Tours (France); Department of Physics, Beijing Institute of Technology, Haidian District, Beijing 100081 (China)
2016-01-28
The Poisson geometry of a discrete string in three dimensional Euclidean space is investigated. For this the Frenet frames are converted into a spinorial representation, the discrete spinor Frenet equation is interpreted in terms of a transfer matrix formalism, and Poisson brackets are introduced in terms of the spinor components. The construction is then generalised, in a self-similar manner, into an infinite hierarchy of Poisson algebras. As an example, the classical Virasoro (Witt) algebra that determines reparametrisation diffeomorphism along a continuous string, is identified as a particular sub-algebra, in the hierarchy of the discrete string Poisson algebra. - Highlights: • Witt (classical Virasoro) algebra is derived in the case of discrete string. • Infinite dimensional hierarchy of Poisson bracket algebras is constructed for discrete strings. • Spinor representation of discrete Frenet equations is developed.
Fluctuating multicomponent lattice Boltzmann model.
Belardinelli, D; Sbragaglia, M; Biferale, L; Gross, M; Varnik, F
2015-02-01
Current implementations of fluctuating lattice Boltzmann equations (FLBEs) describe single component fluids. In this paper, a model based on the continuum kinetic Boltzmann equation for describing multicomponent fluids is extended to incorporate the effects of thermal fluctuations. The thus obtained fluctuating Boltzmann equation is first linearized to apply the theory of linear fluctuations, and expressions for the noise covariances are determined by invoking the fluctuation-dissipation theorem directly at the kinetic level. Crucial for our analysis is the projection of the Boltzmann equation onto the orthonormal Hermite basis. By integrating in space and time the fluctuating Boltzmann equation with a discrete number of velocities, the FLBE is obtained for both ideal and nonideal multicomponent fluids. Numerical simulations are specialized to the case where mean-field interactions are introduced on the lattice, indicating a proper thermalization of the system.
Learning thermodynamics with Boltzmann machines
Torlai, Giacomo; Melko, Roger G.
2016-10-01
A Boltzmann machine is a stochastic neural network that has been extensively used in the layers of deep architectures for modern machine learning applications. In this paper, we develop a Boltzmann machine that is capable of modeling thermodynamic observables for physical systems in thermal equilibrium. Through unsupervised learning, we train the Boltzmann machine on data sets constructed with spin configurations importance sampled from the partition function of an Ising Hamiltonian at different temperatures using Monte Carlo (MC) methods. The trained Boltzmann machine is then used to generate spin states, for which we compare thermodynamic observables to those computed by direct MC sampling. We demonstrate that the Boltzmann machine can faithfully reproduce the observables of the physical system. Further, we observe that the number of neurons required to obtain accurate results increases as the system is brought close to criticality.
Training Restricted Boltzmann Machines
Fischer, Asja
Restricted Boltzmann machines (RBMs) are probabilistic graphical models that can also be interpreted as stochastic neural networks. Training RBMs is known to be challenging. Computing the likelihood of the model parameters or its gradient is in general computationally intensive. Thus, training...... relies on sampling based approximations of the log-likelihood gradient. I will present an empirical and theoretical analysis of the bias of these approximations and show that the approximation error can lead to a distortion of the learning process. The bias decreases with increasing mixing rate...... of the applied sampling procedure and I will introduce a transition operator that leads to faster mixing. Finally, a different parametrisation of RBMs will be discussed that leads to better learning results and more robustness against changes in the data representation....
Lattice Boltzmann model for Coulomb-driven flows in dielectric liquids.
Luo, Kang; Wu, Jian; Yi, Hong-Liang; Tan, He-Ping
2016-02-01
In this paper, we developed a unified lattice Boltzmann model (LBM) to simulate electroconvection in a dielectric liquid induced by unipolar charge injection. Instead of solving the complex set of coupled Navier-Stokes equations, the charge conservation equation, and the Poisson equation of electric potential, three consistent lattice Boltzmann equations are formulated. Numerical results are presented for both strong and weak injection regimes, and different scenarios for the onset and evolution of instability, bifurcation, and chaos are tracked. All LBM results are found to be highly consistent with the analytical solutions and other numerical work.
The local Poisson hypothesis for solar flares
Wheatland, M S
2001-01-01
The question of whether flares occur as a Poisson process has important consequences for flare physics. Recently Lepreti et al. presented evidence for local departure from Poisson statistics in the Geostationary Operational Environmental Satellite (GOES) X-ray flare catalog. Here it is argued that this effect arises from a selection effect inherent in the soft X-ray observations; namely that the slow decay of enhanced flux following a large flare makes detection of subsequent flares less likely. It is also shown that the power-law tail of the GOES waiting-time distribution varies with the solar cycle. This counts against any intrinsic significance to the appearance of a power law, or to the value of its index.
Modules Over Color Hom-Poisson Algebras
2014-01-01
In this paper we introduce color Hom-Poisson algebras and show that every color Hom-associative algebra has a non-commutative Hom-Poisson algebra structure in which the Hom-Poisson bracket is the commutator bracket. Then we show that color Poisson algebras (respectively morphism of color Poisson algebras) turn to color Hom-Poisson algebras (respectively morphism of Color Hom-Poisson algebras) by twisting the color Poisson structure. Next we prove that modules over color Hom–associative algebr...
A hierarchy of Poisson brackets
Pavelka, Michal; Esen, Ogul; Grmela, Miroslav
2015-01-01
The vector field generating reversible time evolution of macroscopic systems involves two ingredients: gradient of a potential (a covector) and a degenerate Poisson structure transforming the covector into a vector. The Poisson structure is conveniently expressed in Poisson brackets, its degeneracy in their Casimirs (i.e. potentials whose gradients produce no vector field). In this paper we investigate in detail hierarchies of Poisson brackets, together with their Casimirs, that arise in passages from more to less detailed (i.e. more macroscopic) descriptions. In particular, we investigate the passage from mechanics of particles (in its Liouville representation) to the reversible kinetic theory and the passage from the reversible kinetic theory to the reversible fluid mechanics. From the physical point of view, the investigation includes binary mixtures and two-point formulations suitable for describing turbulent flows. From the mathematical point of view, we reveal the Lie algebra structure involved in the p...
Gauging the Poisson sigma model
Zucchini, Roberto
2008-01-01
We show how to carry out the gauging of the Poisson sigma model in an AKSZ inspired formulation by coupling it to the a generalization of the Weil model worked out in ref. arXiv:0706.1289 [hep-th]. We call the resulting gauged field theory, Poisson--Weil sigma model. We study the BV cohomology of the model and show its relation to Hamiltonian basic and equivariant Poisson cohomology. As an application, we carry out the gauge fixing of the pure Weil model and of the Poisson--Weil model. In the first case, we obtain the 2--dimensional version of Donaldson--Witten topological gauge theory, describing the moduli space of flat connections on a closed surface. In the second case, we recover the gauged A topological sigma model worked out by Baptista describing the moduli space of solutions of the so--called vortex equations.
KOMPUTASI DISTRIBUSI NEUTRON DALAM STATISTIK MAXWELL BOLTZMANN
Tuti Purwoningsih
2013-03-01
Full Text Available The migration of neutron is arranged by some probability distributions such as probability of spread distribution, probability of distance distribution, probability of energy distribution and probability of flux distribution. One application of these pattern distributions is modelling the reaction between neutron and elements which compose the tissue related to the absorption of neutron in brain cancer tissues. This article explores computation analysis of pattern of distribution of neutron flux in a reactor system. Variables were the amount of neutron simulated and the depth of cylindrical reactor system. Simulations showed that 20-120 minutes was needed in executing 100,000 neutrons to build the distribution pattern of neutrons flux. This pattern was also depended on the depth of the system. In all depths, the peak of neutron flux distribution pattern was in the 3rd bin. Comparison between this simulations and experiment results in literatures showed that by analyzing the simulation of the distribution of neutron flux, a Poisson distribution which follows the Maxwell-Boltzmann was resulted. Perpindahan neutron diatur dengan beberapa peluang distribusi, seperti peluang distribusi sudut hamburan, peluang distribusi jarak perpindahan, peluang distribusi energi transfer, serta peluang distribusi fluks neutron. Salah satu aplikasi dari pola distribusi ini adalah pemodelan reaksi antara neutron dengan elemen-elemen penyusun jaringan yang terkait dengan serapan neutron dan dosis yang terserap oleh jaringan tumor otak pada terapi BNCT (Boron Neutron Capture Therapy. Dalam penelitian ini dibahas analisis komputasi tentang pola distribusi fluks neutron dalam suatu sistem reaktor. Variabel dalam penelitian ini adalah banyaknya neutron yang disimulasikan, serta kedalaman sistem reaktor yang dalam penelitian ini menggunakan sistem reaktor berbentuk silinder. Hasil simulasi menunjukkan bahwa dengan neutron sebanyak 100.000 diperlukan waktu eksekusi sekitar
Coordination of Conditional Poisson Samples
Grafström Anton
2015-12-01
Full Text Available Sample coordination seeks to maximize or to minimize the overlap of two or more samples. The former is known as positive coordination, and the latter as negative coordination. Positive coordination is mainly used for estimation purposes and to reduce data collection costs. Negative coordination is mainly performed to diminish the response burden of the sampled units. Poisson sampling design with permanent random numbers provides an optimum coordination degree of two or more samples. The size of a Poisson sample is, however, random. Conditional Poisson (CP sampling is a modification of the classical Poisson sampling that produces a fixed-size πps sample. We introduce two methods to coordinate Conditional Poisson samples over time or simultaneously. The first one uses permanent random numbers and the list-sequential implementation of CP sampling. The second method uses a CP sample in the first selection and provides an approximate one in the second selection because the prescribed inclusion probabilities are not respected exactly. The methods are evaluated using the size of the expected sample overlap, and are compared with their competitors using Monte Carlo simulation. The new methods provide a good coordination degree of two samples, close to the performance of Poisson sampling with permanent random numbers.
Crystallographic Lattice Boltzmann Method
Namburi, Manjusha; Krithivasan, Siddharth; Ansumali, Santosh
2016-01-01
Current approaches to Direct Numerical Simulation (DNS) are computationally quite expensive for most realistic scientific and engineering applications of Fluid Dynamics such as automobiles or atmospheric flows. The Lattice Boltzmann Method (LBM), with its simplified kinetic descriptions, has emerged as an important tool for simulating hydrodynamics. In a heterogeneous computing environment, it is often preferred due to its flexibility and better parallel scaling. However, direct simulation of realistic applications, without the use of turbulence models, remains a distant dream even with highly efficient methods such as LBM. In LBM, a fictitious lattice with suitable isotropy in the velocity space is considered to recover Navier-Stokes hydrodynamics in macroscopic limit. The same lattice is mapped onto a cartesian grid for spatial discretization of the kinetic equation. In this paper, we present an inverted argument of the LBM, by making spatial discretization as the central theme. We argue that the optimal spatial discretization for LBM is a Body Centered Cubic (BCC) arrangement of grid points. We illustrate an order-of-magnitude gain in efficiency for LBM and thus a significant progress towards feasibility of DNS for realistic flows. PMID:27251098
Nauenberg, Michael
2005-03-01
In 1916 Einstein published a remarkable paper entitled ``On the Quantum Theory of Radiation''ootnotetextA. Einstein ``On the Quantum theory of Radiation,'' Phys. Zeitschrift 18 (1917) 121. First printed in Mitteilungender Physikalischen Gesellschaft Zurich. No 18, 1916. Translated into English in Van der Waerden ``Sources of Quantum Mechanics'' (North Holland 1967) pp. 63-77. in which he obtained Planck's formula for black-body radiation by introducing a new statistical hypothesis for the emmision and absorption of electromagneic radiation based on discrete bundles of energy and momentum which are now called photons. Einstein radiation theory replaced Maxwell's classical theory by a stochastic process which, when properly interpreted, also gives well known statistics of massless particles with even spin.^2 This quantum distribution, however, was not discovered by Einstein but was communicated to him by Bose in 1924. Like Boltzmann's classical counterpart, Einstein's statistical theory leads to an irreversible approach to thermal equilibrium, but because this violates time reversal, Einstein theory can not be regarded as a fundamental theory of physical process.ootnotetextM. Nauenberg ``The evolution of radiation towards thermal equilibrium: A soluble model which illustrates the foundations of statistical mechanics,'' American Journal of Physics 72 (2004) 313 Apparently Einstein and his contemporaries were unaware of this problem, and even today this problem is ignored in contemporary discussions of Einstein's treatment of the black-body spectrum.
Application of lattice Boltzmann scheme to nanofluids
XUAN Yimin; LI Qiang; YAO Zhengping
2004-01-01
A nanofluid is a particle suspension that consists of base liquids and nanoparticles. Nanofluid has greater potential for heat transfer enhancement than traditional solid-liquid mixture. By accounting for the external and internal forces acting on the suspended nanoparticles and interactions among the nanoparticles and fluid particles,a lattice Boltzmann model for simulating flow and energy transport processes inside the nanofluids is proposed. The irregular motion of the nanoparticles and inherent dynamic behavior of nanofluids are discussed. The distributions of suspended nanoparticles inside nanofluids are calculated.
Analysis of Jeans instability from Boltzmann equation
Kremer, Gilberto M
2015-01-01
The dynamics of self-gravitating fluids is analyzed within the framework of a collisionless Boltzmann equation in the presence of gravitational fields and Poisson equation. The equilibrium distribution function takes into account the expansion of the Universe and a pressureless fluid in the matter dominated Universe. Without invoking Jeans "swindle" a dispersion relation is obtained by considering small perturbations of the equilibrium values of the distribution function and gravitational potential. The collapse criterion -- which happens in an unstable region where the solution grows exponentially with time -- is determined from the dispersion relation. The collapse criterion in a static Universe occurs when the wavenumber $k$ is smaller than the Jeans wavenumber $k_J$, which was the solution found by Jeans. For an expanding Universe it is shown that this criterion is $k\\leq\\sqrt{7/6}\\,k_J$. As a consequence the ratio of the mass contained in a sphere of diameter equal to the wavelength $\\lambda=2\\pi/k$ to t...
Poisson–Boltzmann versus Size-Modified Poisson–Boltzmann Electrostatics Applied to Lipid Bilayers
2015-01-01
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. PMID:25426875
Time-Changed Poisson Processes
Kumar, A; Vellaisamy, P
2011-01-01
We consider time-changed Poisson processes, and derive the governing difference-differential equations (DDE) these processes. In particular, we consider the time-changed Poisson processes where the the time-change is inverse Gaussian, or its hitting time process, and discuss the governing DDE's. The stable subordinator, inverse stable subordinator and their iterated versions are also considered as time-changes. DDE's corresponding to probability mass functions of these time-changed processes are obtained. Finally, we obtain a new governing partial differential equation for the tempered stable subordinator of index $0<\\beta<1,$ when $\\beta $ is a rational number. We then use this result to obtain the governing DDE for the mass function of Poisson process time-changed by tempered stable subordinator. Our results extend and complement the results in Baeumer et al. \\cite{B-M-N} and Beghin et al. \\cite{BO-1} in several directions.
Stabilizing the thermal lattice Boltzmann method by spatial filtering.
Gillissen, J J J
2016-10-01
We propose to stabilize the thermal lattice Boltzmann method by filtering the second- and third-order moments of the collision operator. By means of the Chapman-Enskog expansion, we show that the additional numerical diffusivity diminishes in the low-wavnumber limit. To demonstrate the enhanced stability, we consider a three-dimensional thermal lattice Boltzmann system involving 33 discrete velocities. Filtering extends the linear stability of this thermal lattice Boltzmann method to 10-fold smaller transport coefficients. We further demonstrate that the filtering does not compromise the accuracy of the hydrodynamics by comparing simulation results to reference solutions for a number of standardized test cases, including natural convection in two dimensions.
Temperature based Restricted Boltzmann Machines.
Li, Guoqi; Deng, Lei; Xu, Yi; Wen, Changyun; Wang, Wei; Pei, Jing; Shi, Luping
2016-01-13
Restricted Boltzmann machines (RBMs), which apply graphical models to learning probability distribution over a set of inputs, have attracted much attention recently since being proposed as building blocks of multi-layer learning systems called deep belief networks (DBNs). Note that temperature is a key factor of the Boltzmann distribution that RBMs originate from. However, none of existing schemes have considered the impact of temperature in the graphical model of DBNs. In this work, we propose temperature based restricted Boltzmann machines (TRBMs) which reveals that temperature is an essential parameter controlling the selectivity of the firing neurons in the hidden layers. We theoretically prove that the effect of temperature can be adjusted by setting the parameter of the sharpness of the logistic function in the proposed TRBMs. The performance of RBMs can be improved by adjusting the temperature parameter of TRBMs. This work provides a comprehensive insights into the deep belief networks and deep learning architectures from a physical point of view.
Nomura, Yasunori
2015-01-01
Understanding the observed arrow of time is equivalent, under general assumptions, to explaining why Boltzmann brains do not overwhelm ordinary observers. It is usually thought that this provides a condition on the decay rate of every cosmologically accessible de Sitter vacuum, and that this condition is determined by the production rate of Boltzmann brains calculated using semiclassical theory built on each such vacuum. We argue, based on a recently developed picture of microscopic quantum gravitational degrees of freedom, that this thinking needs to be modified. In particular, depending on the structure of the fundamental theory, the decay rate of a de Sitter vacuum may not have to satisfy any condition except possibly the one imposed by the Poincare recurrence. The framework discussed here also addresses the question of whether a Minkowski vacuum may produce Boltzmann brains.
Anisotropic Poisson Processes of Cylinders
Spiess, Malte
2010-01-01
Main characteristics of stationary anisotropic Poisson processes of cylinders (dilated k-dimensional flats) in d-dimensional Euclidean space are studied. Explicit formulae for the capacity functional, the covariance function, the contact distribution function, the volume fraction, and the intensity of the surface area measure are given which can be used directly in applications.
Berezin integrals and Poisson processes
DeAngelis, G. F.; Jona-Lasinio, G.; Sidoravicius, V.
1998-01-01
We show that the calculation of Berezin integrals over anticommuting variables can be reduced to the evaluation of expectations of functionals of Poisson processes via an appropriate Feynman-Kac formula. In this way the tools of ordinary analysis can be applied to Berezin integrals and, as an example, we prove a simple upper bound. Possible applications of our results are briefly mentioned.
Test of Poisson Failure Assumption.
1982-09-01
o. ....... 37 00/ D itlr.: DVI r TEST OF POISSON FAILURE ASSUMPTION Chapter 1. INTRODUCTION 1.1 Background. In stockage models... precipitates a regular failure pattern; it is also possible that the coding of scheduled vs unscheduled does not reflect what we would expect. Data
Sparse Poisson noisy image deblurring.
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.
Non-Boltzmann behavior from the Boltzmann equation
Hagen, M.H.J.; Lowe, C.P.; Frenkel, D.
1995-01-01
We compute the stress autocorrelation function in a two- and three-dimensional system by using the lattice-Boltzmann method. The algebraic long-time behavior ∼t-d/2 in the stress correlation function is clearly observed. The amplitude of this tail is compared with the mode-coupling expression for
Lattice Boltzmann solver of Rossler equation
GuangwuYAN; LiRUAN
2000-01-01
We proposed a lattice Boltzmann model for the Rossler equation. Using a method of multiscales in the lattice Boltzmann model, we get the diffusion reaction as a special case. If the diffusion effect disappeared, we can obtain the lattice Boltzmann solution of the Rossler equation on the mesescopic scale. The numerical results show the method can be used to simulate Rossler equation.
Biesheuvel, P.M.; Veen, van der M.; Norde, W.
2005-01-01
The equilibrium adsorption of polyelectrolytes with multiple types of ionizable groups is described using a modified Poisson-Boltzmann equation including charge regulation of both the polymer and the interface. A one-dimensional mean-field model is used in which the electrostatic potential is
Poisson vs. Long-Tailed Internet traffic
2005-01-01
In this thesis, we reexamine the long discussion on which model is suitable for studying Internet traffic: Poisson or Long-tailed Internet traffic. Poisson model, adapted from telephone network, has been used since the beginning of World Wide Web, while long-tailed distribution gradually takes over with believable evidence. Instead of using Superposition of Point Processes to explain why traffic that is not Poisson tends towards Poisson traffic as the load increases, as it is recent...
The Degraded Poisson Wiretap Channel
Laourine, Amine
2010-01-01
Providing security guarantees for wireless communication is critically important for today's applications. While previous work in this area has concentrated on radio frequency (RF) channels, providing security guarantees for RF channels is inherently difficult because they are prone to rapid variations due small scale fading. Wireless optical communication, on the other hand, is inherently more secure than RF communication due to the intrinsic aspects of the signal propagation in the optical and near-optical frequency range. In this paper, secure communication over wireless optical links is examined by studying the secrecy capacity of a direct detection system. For the degraded Poisson wiretap channel, a closed-form expression of the secrecy capacity is given. A complete characterization of the general rate-equivocation region is also presented. For achievability, an optimal code is explicitly constructed by using the structured code designed by Wyner for the Poisson channel. The converse is proved in two dif...
Perturbation analysis of Poisson processes
Last, Günter
2012-01-01
We consider a Poisson process $\\Phi$ on a general phase space. The expectation of a function of $\\Phi$ can be considered as a functional of the intensity measure $\\lambda$ of $\\Phi$. Extending ealier results of Molchanov and Zuyev (2000) on finite Poisson processes, we study the behaviour of this functional under signed (possibly infinite) perturbations of $\\lambda$. In particular we obtain general Margulis--Russo type formulas for the derivative with respect to non-linear transformations of the intensity measure depending on some parameter. As an application we study the behaviour of expectations of functions of multivariate pure jump L\\'evy processes under perturbations of the L\\'evy measure. A key ingredient of our approach is the explicit Fock space representation obtained in Last and Penrose (2011).
A generalized gyrokinetic Poisson solver
Lin, Z.; Lee, W.W.
1995-03-01
A generalized gyrokinetic Poisson solver has been developed, which employs local operations in the configuration space to compute the polarization density response. The new technique is based on the actual physical process of gyrophase-averaging. It is useful for nonlocal simulations using general geometry equilibrium. Since it utilizes local operations rather than the global ones such as FFT, the new method is most amenable to massively parallel algorithms.
Application of Lattice Boltzmann Methods in Complex Mass Transfer Systems
Sun, Ning
Lattice Boltzmann Method (LBM) is a novel computational fluid dynamics method that can easily handle complex and dynamic boundaries, couple local or interfacial interactions/reactions, and be easily parallelized allowing for simulation of large systems. While most of the current studies in LBM mainly focus on fluid dynamics, however, the inherent power of this method makes it an ideal candidate for the study of mass transfer systems involving complex/dynamic microstructures and local reactions. In this thesis, LBM is introduced to be an alternative computational method for the study of electrochemical energy storage systems (Li-ion batteries (LIBs) and electric double layer capacitors (EDLCs)) and transdermal drug design on mesoscopic scale. Based on traditional LBM, the following in-depth studies have been carried out: (1) For EDLCs, the simulation of diffuse charge dynamics is carried out for both the charge and the discharge processes on 2D systems of complex random electrode geometries (pure random, random spheres and random fibers). Steric effect of concentrated solutions is considered by using modified Poisson-Nernst-Plank (MPNP) equations and compared with regular Poisson-Nernst-Plank (PNP) systems. The effects of electrode microstructures (electrode density, electrode filler morphology, filler size, etc.) on the net charge distribution and charge/discharge time are studied in detail. The influence of applied potential during discharging process is also discussed. (2) For the study of dendrite formation on the anode of LIBs, it is shown that the Lattice Boltzmann model can capture all the experimentally observed features of microstructure evolution at the anode, from smooth to mossy to dendritic. The mechanism of dendrite formation process in mesoscopic scale is discussed in detail and compared with the traditional Sand's time theories. It shows that dendrite formation is closely related to the inhomogeneous reactively at the electrode-electrolyte interface
Quantum corrections for Boltzmann equation
M.; Levy; PETER
2008-01-01
We present the lowest order quantum correction to the semiclassical Boltzmann distribution function,and the equation satisfied by this correction is given. Our equation for the quantum correction is obtained from the conventional quantum Boltzmann equation by explicitly expressing the Planck constant in the gradient approximation,and the quantum Wigner distribution function is expanded in pow-ers of Planck constant,too. The negative quantum correlation in the Wigner dis-tribution function which is just the quantum correction terms is naturally singled out,thus obviating the need for the Husimi’s coarse grain averaging that is usually done to remove the negative quantum part of the Wigner distribution function. We also discuss the classical limit of quantum thermodynamic entropy in the above framework.
Student understanding of the Boltzmann factor
Smith, Trevor I; Thompson, John R
2015-01-01
We present results of our investigation into student understanding of the physical significance and utility of the Boltzmann factor in several simple models. We identify various justifications, both correct and incorrect, that students use when answering written questions that require application of the Boltzmann factor. Results from written data as well as teaching interviews suggest that many students can neither recognize situations in which the Boltzmann factor is applicable, nor articulate the physical significance of the Boltzmann factor as an expression for multiplicity, a fundamental quantity of statistical mechanics. The specific student difficulties seen in the written data led us to develop a guided-inquiry tutorial activity, centered around the derivation of the Boltzmann factor, for use in undergraduate statistical mechanics courses. We report on the development process of our tutorial, including data from teaching interviews and classroom observations on student discussions about the Boltzmann f...
Are there Boltzmann brains in the vacuum
Davenport, Matthew
2010-01-01
"Boltzmann brains" are human brains that arise as thermal or quantum fluctuations and last at least long enough to think a few thoughts. In many scenarios involving universes of infinite size or duration, Boltzmann brains are infinitely more common than human beings who arise in the ordinary way. Thus we should expect to be Boltzmann brains, in contradiction to observation. We discuss here the question of whether Boltzmann brains can arise as quantum fluctuations in the vacuum. Such Boltzmann brains pose an even worse problem than those arising as fluctuations in the thermal state of an exponentially expanding universe. We give several arguments for and against inclusion of vacuum Boltzmann brains in the anthropic reference class, but find neither choice entirely satisfactory.
Poisson Manifolds, Lie Algebroids, Modular Classes: a Survey
Yvette Kosmann-Schwarzbach
2008-01-01
Full Text Available After a brief summary of the main properties of Poisson manifolds and Lie algebroids in general, we survey recent work on the modular classes of Poisson and twisted Poisson manifolds, of Lie algebroids with a Poisson or twisted Poisson structure, and of Poisson-Nijenhuis manifolds. A review of the spinor approach to the modular class concludes the paper.
Boltzmann Transport in Hybrid PIC HET Modeling
2015-07-01
Paper 3. DATES COVERED (From - To) July 2015-July 2015 4. TITLE AND SUBTITLE Boltzmann transport in hybrid PIC HET modeling 5a. CONTRACT NUMBER In...produced a variety of self-consistent electron swarm codes, such as the Magboltz code, focused on directly solving the steady Boltzmann trans-port...Std. 239.18 Boltzmann transport in hybrid PIC HET modeling IEPC-2015- /ISTS-2015-b- Presented at Joint Conference of 30th International
Quasineutral limit of the Vlasov-Poisson system with massless electrons
Han-Kwan, Daniel
2010-01-01
In this paper, we study the quasineutral limit (in other words the limit when the Debye length tends to zero) of Vlasov-Poisson like equations describing the behaviour of ions in a plasma. We consider massless electrons, with a charge density following a Maxwell-Boltzmann law. For cold ions, using the relative entropy method, we derive the classical Isothermal Euler or the (inviscid) Shallow Water systems from fluid mechanics. In a second time, we study the combined quasineutral and strong magnetic field regime for such plasmas.
Large deviations for fractional Poisson processes
Beghin, Luisa
2012-01-01
We present large deviation results for two versions of fractional Poisson processes: the main version which is a renewal process, and the alternative version where all the random variables are weighted Poisson distributed. We also present a sample path large deviation result for suitably normalized counting processes; finally we show how this result can be applied to the two versions of fractional Poisson processes considered in this paper.
Student Understanding of the Boltzmann Factor
Smith, Trevor I.; Mountcastle, Donald B.; Thompson, John R.
2015-01-01
We present results of our investigation into student understanding of the physical significance and utility of the Boltzmann factor in several simple models. We identify various justifications, both correct and incorrect, that students use when answering written questions that require application of the Boltzmann factor. Results from written data…
Lattice Boltzmann equation for relativistic quantum mechanics.
Succi, Sauro
2002-03-15
Relativistic versions of the quantum lattice Boltzmann equation are discussed. It is shown that the inclusion of nonlinear interactions requires the standard collision operator to be replaced by a pair of dynamic fields coupling to the relativistic wave function in a way which can be described by a multicomponent complex lattice Boltzmann equation.
SIMPLE LATTICE BOLTZMANN MODEL FOR TRAFFIC FLOWS
Yan Guangwu; Hu Shouxin
2000-01-01
A lattice Boltzmann model with 5-bit lattice for traffic flows is proposed.Using the Chapman-Enskog expansion and multi-scale technique,we obtain the higher-order moments of equilibrium distribution function.A simple traffic light problem is simulated by using the present lattice Boltzmann model,and the result agrees well with analytical solution.
Wang Jiu Li; Fan Song Hua; Yang Wu Bao; Yang Size
2002-01-01
Based on authors' recently proposed grid-enhanced plasma source ion implantation (GEPSII) technique for inner surface modification of materials with cylindrical geometry, the authors present the corresponding theoretical studies of the temporal evolution of the plasma ion sheath between the grid electrode and the target in a cylindrical bore. Typical results such as the ion sheath evolution, time-dependent ion density and time-integrated ion energy distribution at the target are calculated by solving Poisson's equation coupled with fluid equations for collisionless ions and Boltzmann assumption for electrons using finite difference methods. The calculated results can further verify the feasibility and superiority of this new technique
The Einstein-Boltzmann system and positivity
Lee, Ho
2012-01-01
The Einstein-Boltzmann system is studied, with particular attention to the non-negativity of the solution of the Boltzmann equation. A new parametrization of post-collisional momenta in general relativity is introduced and then used to simplify the conditions on the collision cross-section given by Bancel and Choquet-Bruhat. The non-negativity of solutions of the Boltzmann equation on a given curved spacetime has been studied by Bichteler and by Tadmon. By examining to what extent the results of these authors apply in the framework of Bancel and Choquet-Bruhat, the non-negativity problem for the Einstein-Boltzmann system is resolved for a certain class of scattering kernels. It is emphasized that it is a challenge to extend the existing theory of the Cauchy problem for the Einstein-Boltzmann system so as to include scattering kernels which are physically well-motivated.
Rigid body dynamics on the Poisson torus
Richter, Peter H.
2008-11-01
The theory of rigid body motion with emphasis on the modifications introduced by a Cardan suspension is outlined. The configuration space is no longer SO(3) but a 3-torus; the equivalent of the Poisson sphere, after separation of an angular variable, is a Poisson torus. Iso-energy surfaces and their bifurcations are discussed. A universal Poincaré section method is proposed.
Poisson Geometry from a Dirac perspective
Meinrenken, Eckhard
2016-01-01
We present proofs of classical results in Poisson geometry using techniques from Dirac geometry. This article is based on mini-courses at the Poisson summer school in Geneva, June 2016, and at the workshop "Quantum Groups and Gravity" at the University of Waterloo, April 2016.
Speech parts as Poisson processes.
Badalamenti, A F
2001-09-01
This paper presents evidence that six of the seven parts of speech occur in written text as Poisson processes, simple or recurring. The six major parts are nouns, verbs, adjectives, adverbs, prepositions, and conjunctions, with the interjection occurring too infrequently to support a model. The data consist of more than the first 5000 words of works by four major authors coded to label the parts of speech, as well as periods (sentence terminators). Sentence length is measured via the period and found to be normally distributed with no stochastic model identified for its occurrence. The models for all six speech parts but the noun significantly distinguish some pairs of authors and likewise for the joint use of all words types. Any one author is significantly distinguished from any other by at least one word type and sentence length very significantly distinguishes each from all others. The variety of word type use, measured by Shannon entropy, builds to about 90% of its maximum possible value. The rate constants for nouns are close to the fractions of maximum entropy achieved. This finding together with the stochastic models and the relations among them suggest that the noun may be a primitive organizer of written text.
Thermal cascaded lattice Boltzmann method
Fei, Linlin
2016-01-01
In this paper, a thermal cascaded lattice Boltzmann method (TCLBM) is developed in combination with the double-distribution-function (DDF) approach. A density distribution function relaxed by the cascaded scheme is employed to solve the flow field, and a total energy distribution function relaxed by the BGK scheme is used to solve temperature field, where two distribution functions are coupled naturally. The forcing terms are incorporated by means of central moments, which is consistent with the previous force scheme [Premnath \\emph{et al.}, Phys. Rev. E \\textbf{80}, 036702 (2009)] but the derivation is more intelligible and the evolution process is simpler. In the method, the viscous heat dissipation and compression work are taken into account, the Prandtl number and specific-heat ratio are adjustable, the external force is considered directly without the Boussinesq assumption, and the low-Mach number compressible flows can also be simulated. The forcing scheme is tested by simulating a steady Taylor-Green f...
An Infinite Restricted Boltzmann Machine.
Côté, Marc-Alexandre; Larochelle, Hugo
2016-07-01
We present a mathematical construction for the restricted Boltzmann machine (RBM) that does not require specifying the number of hidden units. In fact, the hidden layer size is adaptive and can grow during training. This is obtained by first extending the RBM to be sensitive to the ordering of its hidden units. Then, with a carefully chosen definition of the energy function, we show that the limit of infinitely many hidden units is well defined. As with RBM, approximate maximum likelihood training can be performed, resulting in an algorithm that naturally and adaptively adds trained hidden units during learning. We empirically study the behavior of this infinite RBM, showing that its performance is competitive to that of the RBM, while not requiring the tuning of a hidden layer size.
Pruning Boltzmann networks and hidden Markov models
Pedersen, Morten With; Stork, D.
1996-01-01
We present sensitivity-based pruning algorithms for general Boltzmann networks. Central to our methods is the efficient calculation of a second-order approximation to the true weight saliencies in a cross-entropy error. Building upon previous work which shows a formal correspondence between linear...... Boltzmann chains and hidden Markov models (HMMs), we argue that our method can be applied to HMMs as well. We illustrate pruning on Boltzmann zippers, which are equivalent to two HMMs with cross-connection links. We verify that our second-order approximation preserves the rank ordering of weight saliencies...
Multiphase lattice Boltzmann methods theory and application
Huang, Haibo; Lu, Xiyun
2015-01-01
Theory and Application of Multiphase Lattice Boltzmann Methods presents a comprehensive review of all popular multiphase Lattice Boltzmann Methods developed thus far and is aimed at researchers and practitioners within relevant Earth Science disciplines as well as Petroleum, Chemical, Mechanical and Geological Engineering. Clearly structured throughout, this book will be an invaluable reference on the current state of all popular multiphase Lattice Boltzmann Methods (LBMs). The advantages and disadvantages of each model are presented in an accessible manner to enable the reader to choose the
Full characterization of the fractional Poisson process
Politi, Mauro; Scalas, Enrico
2011-01-01
The fractional Poisson process (FPP) is a counting process with independent and identically distributed inter-event times following the Mittag-Leffler distribution. This process is very useful in several fields of applied and theoretical physics including models for anomalous diffusion. Contrary to the well-known Poisson process, the fractional Poisson process does not have stationary and independent increments. It is not a L\\'evy process and it is not a Markov process. In this letter, we present formulae for its finite-dimensional distribution functions, fully characterizing the process. These exact analytical results are compared to Monte Carlo simulations.
An introduction to the theory of the Boltzmann equation
Harris, Stewart
2011-01-01
Boltzmann's equation (or Boltzmann-like equations) appears extensively in such disparate fields as laser scattering, solid-state physics, nuclear transport, and beyond the conventional boundaries of physics and engineering, in the fields of cellular proliferation and automobile traffic flow. This introductory graduate-level course for students of physics and engineering offers detailed presentations of the basic modern theory of Boltzmann's equation, including representative applications using both Boltzmann's equation and the model Boltzmann equations developed within the text. It emphasizes
Noncommutative Poisson brackets on Loday algebras and related deformation quantization
UCHINO, Kyousuke
2010-01-01
We introduce a new type of algebra which is called a Loday-Poisson algebra. The class of the Loday-Poisson algebras forms a special subclass of Aguiar's dual-prePoisson algebas (\\cite{A}). We will prove that there exists a unique Loday-Poisson algebra over a Loday algebra, like the Lie-Poisson algebra over a Lie algebra. Thus, Loday-Poisson algebras are regarded as noncommutative analogues of Lie-Poisson algebras. We will show that the polinomial Loday-Poisson algebra is deformation quantizable and that the associated quantum algebra is Loday's associative dialgebra.
Transition from Poisson to circular unitary ensemble
Vinayak; Akhilesh Pandey
2009-09-01
Transitions to universality classes of random matrix ensembles have been useful in the study of weakly-broken symmetries in quantum chaotic systems. Transitions involving Poisson as the initial ensemble have been particularly interesting. The exact two-point correlation function was derived by one of the present authors for the Poisson to circular unitary ensemble (CUE) transition with uniform initial density. This is given in terms of a rescaled symmetry breaking parameter Λ. The same result was obtained for Poisson to Gaussian unitary ensemble (GUE) transition by Kunz and Shapiro, using the contour-integral method of Brezin and Hikami. We show that their method is applicable to Poisson to CUE transition with arbitrary initial density. Their method is also applicable to the more general ℓ CUE to CUE transition where CUE refers to the superposition of ℓ independent CUE spectra in arbitrary ratio.
Poisson point processes imaging, tracking, and sensing
Streit, Roy L
2010-01-01
This overview of non-homogeneous and multidimensional Poisson point processes and their applications features mathematical tools and applications from emission- and transmission-computed tomography to multiple target tracking and distributed sensor detection.
Some Characterizations of Mixed Poisson Processes
Lyberopoulos, D P
2011-01-01
A characterization of mixed Poisson processes in terms of disintegrations is proven. As a consequence some further characterizations of such processes via claim interarrival processes, martingales and claim measures are obtained.
Student understanding of the Boltzmann factor
Smith, Trevor I.; Mountcastle, Donald B.; Thompson, John R.
2015-12-01
[This paper is part of the Focused Collection on Upper Division Physics Courses.] We present results of our investigation into student understanding of the physical significance and utility of the Boltzmann factor in several simple models. We identify various justifications, both correct and incorrect, that students use when answering written questions that require application of the Boltzmann factor. Results from written data as well as teaching interviews suggest that many students can neither recognize situations in which the Boltzmann factor is applicable nor articulate the physical significance of the Boltzmann factor as an expression for multiplicity, a fundamental quantity of statistical mechanics. The specific student difficulties seen in the written data led us to develop a guided-inquiry tutorial activity, centered around the derivation of the Boltzmann factor, for use in undergraduate statistical mechanics courses. We report on the development process of our tutorial, including data from teaching interviews and classroom observations of student discussions about the Boltzmann factor and its derivation during the tutorial development process. This additional information informed modifications that improved students' abilities to complete the tutorial during the allowed class time without sacrificing the effectiveness as we have measured it. These data also show an increase in students' appreciation of the origin and significance of the Boltzmann factor during the student discussions. Our findings provide evidence that working in groups to better understand the physical origins of the canonical probability distribution helps students gain a better understanding of when the Boltzmann factor is applicable and how to use it appropriately in answering relevant questions.
Boltzmann and the art of flying
Dahmen, Silvio R
2007-01-01
One of the less known facets of Ludwig Boltzmann was that of an advocate of Aviation, one of the most challenging technological problems of his times. Boltzmann followed closely the studies of pioneers like Otto Lilienthal in Berlin, and during a lecture on a prestigious conference he vehemently defended further investments in the area. In this article I discuss his involvement with Aviation, his role in its development and his correspondence with two flight pioneers, Otto Lilienthal e Wilhelm Kress.
Lattice Boltzmann approach for complex nonequilibrium flows.
Montessori, A; Prestininzi, P; La Rocca, M; Succi, S
2015-10-01
We present a lattice Boltzmann realization of Grad's extended hydrodynamic approach to nonequilibrium flows. This is achieved by using higher-order isotropic lattices coupled with a higher-order regularization procedure. The method is assessed for flow across parallel plates and three-dimensional flows in porous media, showing excellent agreement of the mass flow with analytical and numerical solutions of the Boltzmann equation across the full range of Knudsen numbers, from the hydrodynamic regime to ballistic motion.
Matrix-valued Quantum Lattice Boltzmann Method
Mendl, Christian B
2013-01-01
We develop a numerical framework for the quantum analogue of the "classical" lattice Boltzmann method (LBM), with the Maxwell-Boltzmann distribution replaced by the Fermi-Dirac function. To accommodate the spin density matrix, the distribution functions become 2x2-matrix valued. We show that the efficient, commonly used BGK approximation of the collision operator is valid in the present setting. The framework could leverage the principles of LBM for simulating complex spin systems, with applications to spintronics.
Modeling Events with Cascades of Poisson Processes
Simma, Aleksandr
2012-01-01
We present a probabilistic model of events in continuous time in which each event triggers a Poisson process of successor events. The ensemble of observed events is thereby modeled as a superposition of Poisson processes. Efficient inference is feasible under this model with an EM algorithm. Moreover, the EM algorithm can be implemented as a distributed algorithm, permitting the model to be applied to very large datasets. We apply these techniques to the modeling of Twitter messages and the revision history of Wikipedia.
Poisson׳s ratio of arterial wall - Inconsistency of constitutive models with experimental data.
Skacel, Pavel; Bursa, Jiri
2016-02-01
Poisson׳s ratio of fibrous soft tissues is analyzed in this paper on the basis of constitutive models and experimental data. Three different up-to-date constitutive models accounting for the dispersion of fibre orientations are analyzed. Their predictions of the anisotropic Poisson׳s ratios are investigated under finite strain conditions together with the effects of specific orientation distribution functions and of other parameters. The applied constitutive models predict the tendency to lower (or even negative) out-of-plane Poisson׳s ratio. New experimental data of porcine arterial layer under uniaxial tension in orthogonal directions are also presented and compared with the theoretical predictions and other literature data. The results point out the typical features of recent constitutive models with fibres concentrated in circumferential-axial plane of arterial layers and their potential inconsistence with some experimental data. The volumetric (in)compressibility of arterial tissues is also discussed as an eventual and significant factor influencing this inconsistency.
Cordier, S.
1995-05-01
In this work a 1-D model of electrons and ions plasma is considered. Electrons are supposed to be in Maxwell-Boltzmann thermodynamic equilibrium while ions are described with an isothermal flow model of charged particles submitted to a self-consistent electric field. A collision term between neutral particles and ions simulates the presence of neutral particles. This work demonstrates the existence of low entropy solutions for this simple model with arbitrary initial conditions. Most of the paper is devoted to the demonstration of this theorem and follows the successive steps: construction of a numerical scheme, recall of the classical properties of Riemann problem solutions using Glimm method, uniform estimations for the whole variation norm, and finally, convergence of the constructed solutions towards a low entropy solution for the non-linear Euler/Poisson system. Domains of application for this type of model are listed in the conclusion. (J.S.). 18 refs.
Boltzmann electron PIC simulation of the E-sail effect
Janhunen, Pekka
2015-01-01
The solar wind electric sail (E-sail) is a planned in-space propulsion device that uses the natural solar wind momentum flux for spacecraft propulsion with the help of long, charged, centrifugally stretched tethers. The problem of accurately predicting the E-sail thrust is still somewhat open, however, due to a possible electron population trapped by the tether. Here we develop a new type of particle-in-cell (PIC) simulation for predicting E-sail thrust. In the new simulation, electrons are modelled as a fluid, hence resembling hydrid simulation, but in contrast to normal hybrid simulation, the Poisson equation is used as in normal PIC to calculate the self-consistent electrostatic field. For electron-repulsive parts of the potential, the Boltzmann relation is used. For electron-attractive parts of the potential we employ a power law which contains a parameter that can be used to control the number of trapped electrons. We perform a set of runs varying the parameter and select the one with the smallest number...
Joe, Harry; Zhu, Rong
2005-04-01
We prove that the generalized Poisson distribution GP(theta, eta) (eta > or = 0) is a mixture of Poisson distributions; this is a new property for a distribution which is the topic of the book by Consul (1989). Because we find that the fits to count data of the generalized Poisson and negative binomial distributions are often similar, to understand their differences, we compare the probability mass functions and skewnesses of the generalized Poisson and negative binomial distributions with the first two moments fixed. They have slight differences in many situations, but their zero-inflated distributions, with masses at zero, means and variances fixed, can differ more. These probabilistic comparisons are helpful in selecting a better fitting distribution for modelling count data with long right tails. Through a real example of count data with large zero fraction, we illustrate how the generalized Poisson and negative binomial distributions as well as their zero-inflated distributions can be discriminated.
Compressed sensing performance bounds under Poisson noise
Raginsky, Maxim; Marcia, Roummel F; Willett, Rebecca M
2009-01-01
This paper describes performance bounds for compressed sensing (CS) where the underlying sparse or compressible (sparsely approximable) signal is a vector of nonnegative intensities whose measurements are corrupted by Poisson noise. In this setting, standard CS techniques cannot be applied directly for several reasons. First, the usual signal-independent and/or bounded noise models do not apply to Poisson noise, which is non-additive and signal-dependent. Second, the CS matrices typically considered are not feasible in real optical systems because they do not adhere to important constraints, such as nonnegativity and photon flux preservation. Third, the typical $\\ell_2$--$\\ell_1$ minimization leads to overfitting in the high-intensity regions and oversmoothing in the low-intensity areas. In this paper, we describe how a feasible positivity- and flux-preserving sensing matrix can be constructed, and then analyze the performance of a CS reconstruction approach for Poisson data that minimizes an objective functi...
The oligarchic structure of Paretian Poisson processes
Eliazar, I.; Klafter, J.
2008-08-01
Paretian Poisson processes are a mathematical model of random fractal populations governed by Paretian power law tail statistics, and connect together and underlie elemental issues in statistical physics. Considering Paretian Poisson processes to represent the wealth of individuals in human populations, we explore their oligarchic structure via the analysis of the following random ratios: the aggregate wealth of the oligarchs ranked from m+1 to n, measured relative to the wealth of the m-th oligarch (n> m). A mean analysis and a stochastic-limit analysis (as n→∞) of these ratios are conducted. We obtain closed-form results which turn out to be highly contingent on the fractal exponent of the Paretian Poisson process considered.
The Space-Fractional Poisson Process
Orsingher, Enzo
2011-01-01
In this paper we introduce the space-fractional Poisson process whose state probabilities $p_k^\\alpha(t)$, $t>0$, $\\alpha \\in (0,1]$, are governed by the equations $(\\mathrm d/\\mathrm dt)p_k(t) = -\\lambda^\\alpha (1-B)p_k^\\alpha(t)$, where $(1-B)^\\alpha$ is the fractional difference operator found in the study of time series analysis. We explicitly obtain the distributions $p_k^\\alpha(t)$, the probability generating functions $G_\\alpha(u,t)$, which are also expressed as distributions of the minimum of i.i.d.\\ uniform random variables. The comparison with the time-fractional Poisson process is investigated and finally, we arrive at the more general space-time fractional Poisson process of which we give the explicit distribution.
Correlated ions in a calcium channel model: a Poisson-Fermi theory.
Liu, Jinn-Liang; Eisenberg, Bob
2013-10-10
We derive a continuum model, called the Poisson-Fermi equation, of biological calcium channels (of cardiac muscle, for example) designed to deal with crowded systems in which ionic species and side chains nearly fill space. The model is evaluated in three dimensions. It includes steric and correlation effects and is derived from classical hard-sphere lattice models of configurational entropy of finite size ions and solvent molecules. The maximum allowable close packing (saturation) condition is satisfied by all ionic species with different sizes and valences in a channel system, as shown theoretically and numerically. Unphysical overcrowding ("divergence") predicted by the Gouy-Chapman diffuse model (produced by a Boltzmann distribution of point charges with large potentials) does not occur with the Fermi-like distribution. Using probability theory, we also provide an analytical description of the implicit dielectric model of ionic solutions that gives rise to a global and a local formula for the chemical potential. In this primitive model, ions are treated as hard spheres and solvent molecules are described as a dielectric medium. The Poisson-Fermi equation is a local formula dealing with different correlations at different places. The correlation effects are apparent in our numerical results. Our results show variations of dielectric permittivity from bath to channel pore described by a new dielectric function derived as an output from the Poisson-Fermi analysis. The results are consistent with existing theoretical and experimental results. The binding curve of Poisson-Fermi is shown to match Monte Carlo data and illustrates the anomalous mole fraction effect of calcium channels, an effective blockage of permeation of sodium ions by a tiny concentration (or number) of calcium ions.
The Isolation Time of Poisson Brownian motions
Peres, Yuval; Stauffer, Alexandre
2011-01-01
Let the nodes of a Poisson point process move independently in $\\R^d$ according to Brownian motions. We study the isolation time for a target particle that is placed at the origin, namely how long it takes until there is no node of the Poisson point process within distance $r$ of it. We obtain asymptotics for the tail probability which are tight up to constants in the exponent in dimension $d\\geq 3$ and tight up to logarithmic factors in the exponent for dimensions $d=1,2$.
Bayesian regression of piecewise homogeneous Poisson processes
Diego Sevilla
2015-12-01
Full Text Available In this paper, a Bayesian method for piecewise regression is adapted to handle counting processes data distributed as Poisson. A numerical code in Mathematica is developed and tested analyzing simulated data. The resulting method is valuable for detecting breaking points in the count rate of time series for Poisson processes. Received: 2 November 2015, Accepted: 27 November 2015; Edited by: R. Dickman; Reviewed by: M. Hutter, Australian National University, Canberra, Australia.; DOI: http://dx.doi.org/10.4279/PIP.070018 Cite as: D J R Sevilla, Papers in Physics 7, 070018 (2015
Phantom cosmology and Boltzmann brains problem
Astashenok, Artyom V; Yurov, Valerian V
2013-01-01
We consider the well-known Boltzmann brains problem in frames of simple phantom energy models with little rip, big rip and big freeze singularity. It is showed that these models (i) satisfy to observational data and (ii) may be free from Boltzmann brains problem. The human observers in phantom models can exist only in during for a certain period $t
How good is the Lattice Boltzmann method?
Kocheemoolayil, Joseph; Barad, Michael; Kiris, Cetin
2016-11-01
Conflicting opinions exist in literature regarding how efficient the lattice Boltzmann method is relative to high-order finite difference approximations of the Navier-Stokes equations on Cartesian meshes, especially at high Mach numbers. We address the question from the pragmatic viewpoint of a practitioner. Dispersion, dissipation and aliasing errors of various lattice Boltzmann models are systematically quantified. The number of floating point operations and memory required for a desired accuracy level are carefully compared for the two numerical methods. Turbulent kinetic energy budgets for several standard test cases such as the decaying Taylor-Green vortex problem are used to evaluate how effective the stabilization mechanisms necessary for lattice Boltzmann method at high Reynolds numbers are. Detailed comments regarding the cyclomatic complexity of the underlying software, scalability of the underlying algorithm on state-of-the-art high-performance computing platforms and wall clock times and relative accuracy for selected simulations conducted using the two approaches are also made.
Hierarchical Boltzmann simulations and model error estimation
Torrilhon, Manuel; Sarna, Neeraj
2017-08-01
A hierarchical simulation approach for Boltzmann's equation should provide a single numerical framework in which a coarse representation can be used to compute gas flows as accurately and efficiently as in computational fluid dynamics, but a subsequent refinement allows to successively improve the result to the complete Boltzmann result. We use Hermite discretization, or moment equations, for the steady linearized Boltzmann equation for a proof-of-concept of such a framework. All representations of the hierarchy are rotationally invariant and the numerical method is formulated on fully unstructured triangular and quadrilateral meshes using a implicit discontinuous Galerkin formulation. We demonstrate the performance of the numerical method on model problems which in particular highlights the relevance of stability of boundary conditions on curved domains. The hierarchical nature of the method allows also to provide model error estimates by comparing subsequent representations. We present various model errors for a flow through a curved channel with obstacles.
Adaptive Lattice Boltzmann Model for Compressible Flows
无
2000-01-01
A new lattice Boltzmann model for compressible flows is presented. The main difference from the standard lattice Boltzmann model is that the particle velocities are no longer constant, but vary with the mean velocity and internal energy. The adaptive nature of the particle velocities permits the mean flow to have a high Mach number. The introduction of a particle potential energy makes the model suitable for a perfect gas with arbitrary specific heat ratio. The Navier-Stokes (N-S) equations are derived by the Chapman-Enskog method from the BGK Boltzmann equation. Two kinds of simulations have been carried out on the hexagonal lattice to test the proposed model. One is the Sod shock-tube simulation. The other is a strong shock of Mach number 5.09 diffracting around a corner.
A one-level FETI method for the drift–diffusion-Poisson system with discontinuities at an interface
Baumgartner, Stefan
2013-06-01
A 3d feti method for the drift-diffusion-Poisson system including discontinuities at a 2d interface is developed. The motivation for this work is to provide a parallel numerical algorithm for a system of PDEs that are the basic model equations for the simulation of semiconductor devices such as transistors and sensors. Moreover, discontinuities or jumps in the potential and its normal derivative at a 2d surface are included for the simulation of nanowire sensors based on a homogenized model. Using the feti method, these jump conditions can be included with the usual numerical properties and the original Farhat-Roux feti method is extended to the drift-diffusion-Poisson equations including discontinuities. We show two numerical examples. The first example verifies the correct implementation including the discontinuities on a 2d grid divided into eight subdomains. The second example is 3d and shows the application of the algorithm to the simulation of nanowire sensors with high aspect ratios. The Poisson-Boltzmann equation and the drift-diffusion-Poisson system with jump conditions are solved on a 3d grid with real-world boundary conditions. © 2013 Elsevier Inc..
Kinetic Boltzmann, Vlasov and Related Equations
Sinitsyn, Alexander; Vedenyapin, Victor
2011-01-01
Boltzmann and Vlasov equations played a great role in the past and still play an important role in modern natural sciences, technique and even philosophy of science. Classical Boltzmann equation derived in 1872 became a cornerstone for the molecular-kinetic theory, the second law of thermodynamics (increasing entropy) and derivation of the basic hydrodynamic equations. After modifications, the fields and numbers of its applications have increased to include diluted gas, radiation, neutral particles transportation, atmosphere optics and nuclear reactor modelling. Vlasov equation was obtained in
Grid refinement for entropic lattice Boltzmann models.
Dorschner, B; Frapolli, N; Chikatamarla, S S; Karlin, I V
2016-11-01
We propose a multidomain grid refinement technique with extensions to entropic incompressible, thermal, and compressible lattice Boltzmann models. Its validity and accuracy are assessed by comparison to available direct numerical simulation and experiment for the simulation of isothermal, thermal, and viscous supersonic flow. In particular, we investigate the advantages of grid refinement for the setups of turbulent channel flow, flow past a sphere, Rayleigh-Bénard convection, as well as the supersonic flow around an airfoil. Special attention is paid to analyzing the adaptive features of entropic lattice Boltzmann models for multigrid simulations.
Grid refinement for entropic lattice Boltzmann models
Dorschner, B; Chikatamarla, S S; Karlin, I V
2016-01-01
We propose a novel multi-domain grid refinement technique with extensions to entropic incompressible, thermal and compressible lattice Boltzmann models. Its validity and accuracy are accessed by comparison to available direct numerical simulation and experiment for the simulation of isothermal, thermal and viscous supersonic flow. In particular, we investigate the advantages of grid refinement for the set-ups of turbulent channel flow, flow past a sphere, Rayleigh-Benard convection as well as the supersonic flow around an airfoil. Special attention is payed to analyzing the adaptive features of entropic lattice Boltzmann models for multi-grid simulations.
Fast lattice Boltzmann solver for relativistic hydrodynamics.
Mendoza, M; Boghosian, B M; Herrmann, H J; Succi, S
2010-07-01
A lattice Boltzmann formulation for relativistic fluids is presented and numerically validated through quantitative comparison with recent hydrodynamic simulations of relativistic fluids. In order to illustrate its capability to handle complex geometries, the scheme is also applied to the case of a three-dimensional relativistic shock wave, generated by a supernova explosion, impacting on a massive interstellar cloud. This formulation opens up the possibility of exporting the proven advantages of lattice Boltzmann methods, namely, computational efficiency and easy handling of complex geometries, to the context of (mildly) relativistic fluid dynamics at large, from quark-gluon plasmas up to supernovae with relativistic outflows.
Celebrating Cercignani's conjecture for the Boltzmann equation
Villani, Cédric
2011-01-01
Cercignani\\'s conjecture assumes a linear inequality between the entropy and entropy production functionals for Boltzmann\\'s nonlinear integral operator in rarefied gas dynamics. Related to the field of logarithmic Sobolev inequalities and spectral gap inequalities, this issue has been at the core of the renewal of the mathematical theory of convergence to thermodynamical equilibrium for rarefied gases over the past decade. In this review paper, we survey the various positive and negative results which were obtained since the conjecture was proposed in the 1980s. © American Institute of Mathematical Sciences.
A class of CTRWs: Compound fractional Poisson processes
Scalas, Enrico
2011-01-01
This chapter is an attempt to present a mathematical theory of compound fractional Poisson processes. The chapter begins with the characterization of a well-known L\\'evy process: The compound Poisson process. The semi-Markov extension of the compound Poisson process naturally leads to the compound fractional Poisson process, where the Poisson counting process is replaced by the Mittag-Leffler counting process also known as fractional Poisson process. This process is no longer Markovian and L\\'evy. However, several analytical results are available and some of them are discussed here. The functional limit of the compound Poisson process is an $\\alpha$-stable L\\'evy process, whereas in the case of the compound fractional Poisson process, one gets an $\\alpha$-stable L\\'evy process subordinated to the fractional Poisson process.
Fluctuating lattice Boltzmann method for the diffusion equation.
Wagner, Alexander J; Strand, Kyle
2016-09-01
We derive a fluctuating lattice Boltzmann method for the diffusion equation. The derivation removes several shortcomings of previous derivations for fluctuating lattice Boltzmann methods for hydrodynamic systems. The comparative simplicity of this diffusive system highlights the basic features of this first exact derivation of a fluctuating lattice Boltzmann method.
Multispeed models in off-lattice Boltzmann simulations
Bardow, A.; Karlin, I.V.; Gusev, A.A.
2008-01-01
The lattice Boltzmann method is a highly promising approach to the simulation of complex flows. Here, we realize recently proposed multispeed lattice Boltzmann models [S. Chikatamarla et al., Phys. Rev. Lett. 97 190601 (2006)] by exploiting the flexibility offered by off-lattice Boltzmann methods.
A Fluctuating Lattice Boltzmann Method for the Diffusion Equation
Wagner, Alexander J
2016-01-01
We derive a fluctuating lattice Boltzmann method for the diffusion equation. The derivation removes several shortcomings of previous derivations for fluctuating lattice Boltzmann methods for hydrodynamic systems. The comparative simplicity of this diffusive system highlights the basic features of this first exact derivation of a fluctuating lattice Boltzmann method.
Affine Poisson Groups and WZW Model
Ctirad Klimcík
2008-01-01
Full Text Available We give a detailed description of a dynamical system which enjoys a Poisson-Lie symmetry with two non-isomorphic dual groups. The system is obtained by taking the q → ∞ limit of the q-deformed WZW model and the understanding of its symmetry structure results in uncovering an interesting duality of its exchange relations.
Transportation inequalities: From Poisson to Gibbs measures
Ma, Yutao; Wang, Xinyu; Wu, Liming; 10.3150/00-BEJ268
2011-01-01
We establish an optimal transportation inequality for the Poisson measure on the configuration space. Furthermore, under the Dobrushin uniqueness condition, we obtain a sharp transportation inequality for the Gibbs measure on $\\mathbb{N}^{\\Lambda}$ or the continuum Gibbs measure on the configuration space.
Poisson boundaries over locally compact quantum groups
Kalantar, Mehrdad; Ruan, Zhong-Jin
2011-01-01
We present versions of several classical results on harmonic functions and Poisson boundaries in the setting of locally compact quantum groups $\\mathbb{G}$. In particular, the Choquet-Deny theorem holds for compact quantum groups; also, the result of Kaimanovich-Vershik and Rosenblatt, which characterizes group amenability in terms of harmonic functions, answering a conjecture by Furstenberg, admits a non-commutative analogue in the separable case. We also explore the relation between classical and quantum Poisson boundaries by investigating the spectrum of the quantum group. We apply this machinery to find a concrete realization of the Poisson boundaries of the compact quantum group $SU_{q}(2)$ arising from measures on its spectrum. We further show that the Poisson boundary of the natural Markov operator extension of the convolution action of a quantum probability measure $\\mu$ on $L_\\infty(\\mathbb{G})$ to $B(L_2(\\mathbb{G}))$, as introduced and studied - for general completely bounded multipliers on $L_1(\\m...
Continental moisture recycling as a Poisson process
H. F. Goessling
2013-04-01
Full Text Available On their journey across large land masses, water molecules experience a number of precipitation-evaporation cycles (recycling events. We derive analytically the frequency distributions of recycling events for the water molecules contained in a given air parcel. Given the validity of certain simplifying assumptions, continental moisture recycling is shown to develop either into a Poisson distribution or a geometric distribution. We distinguish two cases: in case (A recycling events are counted since the water molecules were last advected across the ocean-land boundary. In case (B recycling events are counted since the water molecules were last evaporated from the ocean. For case B we show by means of a simple scale analysis that, given the conditions on Earth, realistic frequency distributions may be regarded as a mixture of a Poisson distribution and a geometric distribution. By contrast, in case A the Poisson distribution generally appears as a reasonable approximation. This conclusion is consistent with the simulation results of an earlier study where an atmospheric general circulation model equipped with water vapor tracers was used. Our results demonstrate that continental moisture recycling can be interpreted as a Poisson process.
Bayesian credible interval construction for Poisson statistics
ZHU Yong-Sheng
2008-01-01
The construction of the Bayesian credible (confidence) interval for a Poisson observable including both the signal and background with and without systematic uncertainties is presented.Introducing the conditional probability satisfying the requirement of the background not larger than the observed events to construct the Bayesian credible interval is also discussed.A Fortran routine,BPOCI,has been developed to implement the calculation.
Thinning spatial point processes into Poisson processes
Møller, Jesper; Schoenberg, Frederic Paik
2010-01-01
are identified, and where we simulate backwards and forwards in order to obtain the thinned process. In the case of a Cox process, a simple independent thinning technique is proposed. In both cases, the thinning results in a Poisson process if and only if the true Papangelou conditional intensity is used, and...
Thinning spatial point processes into Poisson processes
Møller, Jesper; Schoenberg, Frederic Paik
, and where one simulates backwards and forwards in order to obtain the thinned process. In the case of a Cox process, a simple independent thinning technique is proposed. In both cases, the thinning results in a Poisson process if and only if the true Papangelou conditional intensity is used, and thus can...
Evolutionary inference via the Poisson Indel Process.
Bouchard-Côté, Alexandre; Jordan, Michael I
2013-01-22
We address the problem of the joint statistical inference of phylogenetic trees and multiple sequence alignments from unaligned molecular sequences. This problem is generally formulated in terms of string-valued evolutionary processes along the branches of a phylogenetic tree. The classic evolutionary process, the TKF91 model [Thorne JL, Kishino H, Felsenstein J (1991) J Mol Evol 33(2):114-124] is a continuous-time Markov chain model composed of insertion, deletion, and substitution events. Unfortunately, this model gives rise to an intractable computational problem: The computation of the marginal likelihood under the TKF91 model is exponential in the number of taxa. In this work, we present a stochastic process, the Poisson Indel Process (PIP), in which the complexity of this computation is reduced to linear. The Poisson Indel Process is closely related to the TKF91 model, differing only in its treatment of insertions, but it has a global characterization as a Poisson process on the phylogeny. Standard results for Poisson processes allow key computations to be decoupled, which yields the favorable computational profile of inference under the PIP model. We present illustrative experiments in which Bayesian inference under the PIP model is compared with separate inference of phylogenies and alignments.
Computation of confidence intervals for Poisson processes
Aguilar-Saavedra, J. A.
2000-07-01
We present an algorithm which allows a fast numerical computation of Feldman-Cousins confidence intervals for Poisson processes, even when the number of background events is relatively large. This algorithm incorporates an appropriate treatment of the singularities that arise as a consequence of the discreteness of the variable.
Computation of confidence intervals for Poisson processes
Aguilar-Saavedra, J A
2000-01-01
We present an algorithm which allows a fast numerical computation of Feldman-Cousins confidence intervals for Poisson processes, even when the number of background events is relatively large. This algorithm incorporates an appropriate treatment of the singularities that arise as a consequence of the discreteness of the variable.
Exit problems for oscillating compound Poisson process
Kadankova, Tetyana
2011-01-01
In this article we determine the Laplace transforms of the main boundary functionals of the oscillating compound Poisson process. These are the first passage time of the level, the joint distribution of the first exit time from the interval and the value of the overshoot through the boundary. Under certain conditions we establish the asymptotic behaviour of the mentioned functionals.
Homological unimodularity and Calabi-Yau condition for Poisson algebras
Lü, Jiafeng; Wang, Xingting; Zhuang, Guangbin
2017-09-01
In this paper, we show that the twisted Poincaré duality between Poisson homology and cohomology can be derived from the Serre invertible bimodule. This gives another definition of a unimodular Poisson algebra in terms of its Poisson Picard group. We also achieve twisted Poincaré duality for Hochschild (co)homology of Poisson bimodules using rigid dualizing complex. For a smooth Poisson affine variety with the trivial canonical bundle, we prove that its enveloping algebra is a Calabi-Yau algebra if the Poisson structure is unimodular.
The Non-Classical Boltzmann Equation, and Diffusion-Based Approximations to the Boltzmann Equation
Frank, Martin; Larsen, Edward W; Vasques, Richard
2014-01-01
We show that several diffusion-based approximations (classical diffusion or SP1, SP2, SP3) to the linear Boltzmann equation can (for an infinite, homogeneous medium) be represented exactly by a non-classical transport equation. As a consequence, we indicate a method to solve diffusion-based approximations to the Boltzmann equation via Monte Carlo, with only statistical errors - no truncation errors.
Full Boltzmann equations for leptogenesis including scattering
Hahn-Woernle, F; Wong, Y Y Y
2009-01-01
We study the evolution of a cosmological baryon asymmetry produced via leptogenesis by means of the full classical Boltzmann equations, without the assumption of kinetic equilibrium and including all quantum statistical factors. Beginning with the full mode equations we derive the usual equations of motion for the right-handed neutrino number density and integrated lepton asymmetry, and show explicitly the impact of each assumption on these quantities. For the first time, we investigate also the effects of scattering of the right-handed neutrino with the top quark to leading order in the Yukawa couplings by means of the full Boltzmann equations. We find that in our full Boltzmann treatment the final lepton asymmetry can be suppressed by as much as a factor of 1.5 in the weak wash-out regime (K1), the full Boltzmann treatment and the integrated approach give nearly identical final lepton asymmetries (within 10 % of each other at K>3). Finally, we show that the opposing effects of quantum statistics on decays/i...
Stefan-Boltzmann law for massive photons
Moreira, E S
2015-01-01
Thirty years ago a paper appeared in the literature generalizing the Stefan-Boltzmann law to include massive photons. The paper suffers from a flaw though: it assumes that a massive photon travels at the speed of (massless) light. The present work fixes the mistake and presents the correct formula for the radiance.
Stefan-Boltzmann Law for Massive Photons
Moreira, E. S.; Ribeiro, T. G.
2016-08-01
This paper generalizes the Stefan-Boltzmann law to include massive photons. A crucial ingredient to obtain the correct formula for the radiance is to realize that a massive photon does not travel at the speed of (massless) light. It follows that, contrary to what could be expected, the radiance is not proportional to the energy density times the speed of light.
Boltzmann und das Ende des mechanistischen Weltbildes
Renn, Jürgen
2007-01-01
Der Wissenschaftshistoriker und Physiker Jürgen Renn untersucht die Rolle des österreichischen Physikers und Philosophen Ludwig Boltzmann (18441906) bei der Entwicklung der modernen Physik. Boltzmann war einer der letzen Vertreter des mechanistischen Weltbildes und stand somit am Ende eines Zeitalters. Renn porträtiert den Wissenschaftler aber als einen Pionier der modernen Physik, dessen Beschäftigung mit den inneren Spannungen der klassischen Physik ihn visionär zukünftige Fragestellungen aufgreifen ließ. So befasste sich Boltzmann etwa mit den Grenzproblemen zwischen Mechanik und Thermodynamik, die ihn zur Entwicklung immer raffinierterer Instrumente der statistischen Physik antrieb, die schließlich zu Schlüsselinstrumenten der modernen Physik wurden. Boltzmanns Werk steht somit am Übergang vom mechanistischen Weltbild zur Relativitäts- und Quantentheorie. Der Aussage des viel bekannteren Physikers Albert Einstein, dass Fantasie wichtiger sei als Wissen, hält Jürgen Renn im Hinblick auf Leben ...
Entropic lattice Boltzmann model for Burgers's equation.
Boghosian, Bruce M; Love, Peter; Yepez, Jeffrey
2004-08-15
Entropic lattice Boltzmann models are discrete-velocity models of hydrodynamics that possess a Lyapunov function. This feature makes them useful as nonlinearly stable numerical methods for integrating hydrodynamic equations. Over the last few years, such models have been successfully developed for the Navier-Stokes equations in two and three dimensions, and have been proposed as a new category of subgrid model of turbulence. In the present work we develop an entropic lattice Boltzmann model for Burgers's equation in one spatial dimension. In addition to its pedagogical value as a simple example of such a model, our result is actually a very effective way to simulate Burgers's equation in one dimension. At moderate to high values of viscosity, we confirm that it exhibits no trace of instability. At very small values of viscosity, however, we report the existence of oscillations of bounded amplitude in the vicinity of the shock, where gradient scale lengths become comparable with the grid size. As the viscosity decreases, the amplitude at which these oscillations saturate tends to increase. This indicates that, in spite of their nonlinear stability, entropic lattice Boltzmann models may become inaccurate when the ratio of gradient scale length to grid spacing becomes too small. Similar inaccuracies may limit the utility of the entropic lattice Boltzmann paradigm as a subgrid model of Navier-Stokes turbulence.
General relativistic Boltzmann equation, I: Covariant treatment
Debbasch, F.; van Leeuwen, W.A.
2009-01-01
This series of two articles aims at dissipating the rather dense haze existing in the present literature around the General Relativistic Boltzmann equation. In this first article, the general relativistic one-particle distribution function in phase space is defined as an average of delta functions.
Geometric variations of the Boltzmann entropy
Kalogeropoulos, Nikos
2008-01-01
We perform a calculation of the first and second order infinitesimal variations, with respect to energy, of the Boltzmann entropy of constant energy hypersurfaces of a system with a finite number of degrees of freedom. We comment on the stability interpretation of the second variation in this framework.
THREE WAY DECOMPOSITION FOR THE BOLTZMANN EQUATION
Ilgis Ibragimov; Sergej Rjasanow
2009-01-01
The initial value problem for the spatially homogeneous Boltzmann equation is considered. A deterministic numerical scheme for this problem is developed by the use of the three way decomposition of the unknown function as well as of the collision integral. On this way, almost linear complexity of the algorithm is achieved. Some numerical examples are presented.
Boltzmann Samplers for Colored Combinatorial Objects
Bodini, Olivier
2009-01-01
In this paper, we give a general framework for the Boltzmann generation of colored objects belonging to combinatorial constructible classes. We propose an intuitive notion called profiled objects which allows the sampling of size-colored objects (and also of k-colored objects) although the corresponding class cannot be described by an analytic ordinary generating function.
On higher Poisson and Koszul--Schouten brackets
Bruce, Andrew James
2009-01-01
In this note we show how to construct a homotopy BV-algebra on the algebra of differential forms over a higher Poisson manifold. The Lie derivative along the higher Poisson structure provides the generating operator.
On the Confidence Interval for the parameter of Poisson Distribution
Bityukov, S I; Taperechkina, V A
2000-01-01
In present paper the possibility of construction of continuous analogue of Poisson distribution with the search of bounds of confidence intervals for parameter of Poisson distribution is discussed and the results of numerical construction of confidence intervals are presented.
Poisson Bracket on the Space of Histories
Marolf, D
1994-01-01
We extend the Poisson bracket from a Lie bracket of phase space functions to a Lie bracket of functions on the space of canonical histories and investigate the resulting algebras. Typically, such extensions define corresponding Lie algebras on the space of Lagrangian histories via pull back to a space of partial solutions. These are the same spaces of histories studied with regard to path integration and decoherence. Such spaces of histories are familiar from path integration and some studies of decoherence. For gauge systems, we extend both the canonical and reduced Poisson brackets to the full space of histories. We then comment on the use of such algebras in time reparameterization invariant systems and systems with a Gribov ambiguity, though our main goal is to introduce concepts and techniques for use in a companion paper.
Model selection for Poisson processes with covariates
Sart, Mathieu
2011-01-01
We observe $n$ inhomogeneous Poisson processes with covariates and aim at estimating their intensities. To handle this problem, we assume that the intensity of each Poisson process is of the form $s (\\cdot, x)$ where $x$ is the covariate and where $s$ is an unknown function. We propose a model selection approach where the models are used to approximate the multivariate function $s$. We show that our estimator satisfies an oracle-type inequality under very weak assumptions both on the intensities and the models. By using an Hellinger-type loss, we establish non-asymptotic risk bounds and specify them under various kind of assumptions on the target function $s$ such as being smooth or composite. Besides, we show that our estimation procedure is robust with respect to these assumptions.
Stabilities for nonisentropic Euler-Poisson equations.
Cheung, Ka Luen; Wong, Sen
2015-01-01
We establish the stabilities and blowup results for the nonisentropic Euler-Poisson equations by the energy method. By analysing the second inertia, we show that the classical solutions of the system with attractive forces blow up in finite time in some special dimensions when the energy is negative. Moreover, we obtain the stabilities results for the system in the cases of attractive and repulsive forces.
Continental moisture recycling as a Poisson process
2013-01-01
On their journey across large land masses, water molecules experience a number of precipitation-evaporation cycles (recycling events). We derive analytically the frequency distributions of recycling events for the water molecules contained in a given air parcel. Given the validity of certain simplifying assumptions, continental moisture recycling is shown to develop either into a Poisson distribution or a geometric distribution. We distinguish two cases: in case (A) recycling events a...
Continental moisture recycling as a Poisson process
2013-01-01
On their journey over large land masses, water molecules experience a number of precipitation–evaporation cycles (recycling events). We derive analytically the frequency distributions of recycling events for the water molecules contained in a given air parcel. Given the validity of certain simplifying assumptions, the frequency distribution of recycling events is shown to develop either into a Poisson distribution or a geometric distribution. We distingu...
A New Echeloned Poisson Series Processor (EPSP)
Ivanova, Tamara
2001-07-01
A specialized Echeloned Poisson Series Processor (EPSP) is proposed. It is a typical software for the implementation of analytical algorithms of Celestial Mechanics. EPSP is designed for manipulating long polynomial-trigonometric series with literal divisors. The coefficients of these echeloned series are the rational or floating-point numbers. The Keplerian processor and analytical generator of special celestial mechanics functions based on the EPSP are also developed.
Irreversible thermodynamics of Poisson processes with reaction.
Méndez, V; Fort, J
1999-11-01
A kinetic model is derived to study the successive movements of particles, described by a Poisson process, as well as their generation. The irreversible thermodynamics of this system is also studied from the kinetic model. This makes it possible to evaluate the differences between thermodynamical quantities computed exactly and up to second-order. Such differences determine the range of validity of the second-order approximation to extended irreversible thermodynamics.
Irreversible thermodynamics of Poisson processes with reaction
Méndez, Vicenç; Fort, Joaquim
1999-11-01
A kinetic model is derived to study the successive movements of particles, described by a Poisson process, as well as their generation. The irreversible thermodynamics of this system is also studied from the kinetic model. This makes it possible to evaluate the differences between thermodynamical quantities computed exactly and up to second-order. Such differences determine the range of validity of the second-order approximation to extended irreversible thermodynamics.
An alternative hyper-Poisson distribution
C. Satheesh Kumar
2013-05-01
Full Text Available An alternative form of hyper-Poisson distribution is introduced through its probability mass function and studies some of its important aspects such as mean, variance, expressions for its raw moments, factorial moments, probability generating function and recursion formulae for its probabilities, raw moments and factorial moments. The estimation of the parameters of the distribution by various methods are considered and illustrated using some real life data sets.
Development of a Prototype Lattice Boltzmann Code for CFD of Fusion Systems.
Pattison, Martin J; Premnath, Kannan N; Banerjee, Sanjoy; Dwivedi, Vinay
2007-02-26
Designs of proposed fusion reactors, such as the ITER project, typically involve the use of liquid metals as coolants in components such as heat exchangers, which are generally subjected to strong magnetic fields. These fields induce electric currents in the fluids, resulting in magnetohydrodynamic (MHD) forces which have important effects on the flow. The objective of this SBIR project was to develop computational techniques based on recently developed lattice Boltzmann techniques for the simulation of these MHD flows and implement them in a computational fluid dynamics (CFD) code for the study of fluid flow systems encountered in fusion engineering. The code developed during this project, solves the lattice Boltzmann equation, which is a kinetic equation whose behaviour represents fluid motion. This is in contrast to most CFD codes which are based on finite difference/finite volume based solvers. The lattice Boltzmann method (LBM) is a relatively new approach which has a number of advantages compared with more conventional methods such as the SIMPLE or projection method algorithms that involve direct solution of the Navier-Stokes equations. These are that the LBM is very well suited to parallel processing, with almost linear scaling even for very large numbers of processors. Unlike other methods, the LBM does not require solution of a Poisson pressure equation leading to a relatively fast execution time. A particularly attractive property of the LBM is that it can handle flows in complex geometries very easily. It can use simple rectangular grids throughout the computational domain -- generation of a body-fitted grid is not required. A recent advance in the LBM is the introduction of the multiple relaxation time (MRT) model; the implementation of this model greatly enhanced the numerical stability when used in lieu of the single relaxation time model, with only a small increase in computer time. Parallel processing was implemented using MPI and demonstrated the
Alternative Forms of Compound Fractional Poisson Processes
Luisa Beghin
2012-01-01
Full Text Available We study here different fractional versions of the compound Poisson process. The fractionality is introduced in the counting process representing the number of jumps as well as in the density of the jumps themselves. The corresponding distributions are obtained explicitly and proved to be solution of fractional equations of order less than one. Only in the final case treated in this paper, where the number of jumps is given by the fractional-difference Poisson process defined in Orsingher and Polito (2012, we have a fractional driving equation, with respect to the time argument, with order greater than one. Moreover, in this case, the compound Poisson process is Markovian and this is also true for the corresponding limiting process. All the processes considered here are proved to be compositions of continuous time random walks with stable processes (or inverse stable subordinators. These subordinating relationships hold, not only in the limit, but also in the finite domain. In some cases the densities satisfy master equations which are the fractional analogues of the well-known Kolmogorov one.
Differential Poisson Sigma Models with Extended Supersymmetry
Arias, Cesar; Torres-Gomez, Alexander
2016-01-01
The induced two-dimensional topological N=1 supersymmetric sigma model on a differential Poisson manifold M presented in arXiv:1503.05625 is shown to be a special case of the induced Poisson sigma model on the bi-graded supermanifold T[0,1]M. The bi-degree comprises the standard N-valued target space degree, corresponding to the form degree on the worldsheet, and an additional Z-valued fermion number, corresponding to the degree in the differential graded algebra of forms on M. The N=1 supersymmetry stems from the compatibility between the (extended) differential Poisson bracket and the de Rham differential on M. The latter is mapped to a nilpotent vector field Q of bi-degree (0,1) on T*[1,0](T[0,1]M), and the covariant Hamiltonian action is Q-exact. New extended supersymmetries arise as inner derivatives along special bosonic Killing vectors on M that induce Killing supervector fields of bi-degree (0,-1) on T*[1,0](T[0,1]M).
Connectivity in Sub-Poisson Networks
Blaszczyszyn, Bartlomiej
2010-01-01
We consider a class of point processes (pp), which we call {\\em sub-Poisson}; these are pp that can be directionally-convexly ($dcx$) dominated by some Poisson pp. The $dcx$ order has already been shown useful in comparing various point process characteristics, including Ripley's and correlation functions as well as shot-noise fields generated by pp, indicating in particular that smaller in the $dcx$ order processes exhibit more regularity (less clustering, less voids) in the repartition of their points. Using these results, in this paper we study the impact of the $dcx$ ordering of pp on the properties of two continuum percolation models, which have been proposed in the literature to address macroscopic connectivity properties of large wireless networks. As the first main result of this paper, we extend the classical result on the existence of phase transition in the percolation of the Gilbert's graph (called also the Boolean model), generated by a homogeneous Poisson pp, to the class of homogeneous sub-Pois...
Leibniz Color Algebra and Leibniz Poisson Color Algebra%Leibniz Color代数和Leibniz Poisson Color代数
高齐; 王聪; 张庆成
2014-01-01
This paper presents the definition of Leibniz color algebra and Leibniz Poisson color algebra, and the method to construct the Leibniz color algebra and the Leibniz Poisson color algebra by the newly defined product.%定义了Leibniz color代数和 Leibniz Poisson color 代数，并通过新定义的乘法运算得到了构造Leibniz color代数和Leibniz Poisson color代数的方法。
Compositions, Random Sums and Continued Random Fractions of Poisson and Fractional Poisson Processes
Orsingher, Enzo; Polito, Federico
2012-08-01
In this paper we consider the relation between random sums and compositions of different processes. In particular, for independent Poisson processes N α ( t), N β ( t), t>0, we have that N_{α}(N_{β}(t)) stackrel{d}{=} sum_{j=1}^{N_{β}(t)} Xj, where the X j s are Poisson random variables. We present a series of similar cases, where the outer process is Poisson with different inner processes. We highlight generalisations of these results where the external process is infinitely divisible. A section of the paper concerns compositions of the form N_{α}(tauk^{ν}), ν∈(0,1], where tauk^{ν} is the inverse of the fractional Poisson process, and we show how these compositions can be represented as random sums. Furthermore we study compositions of the form Θ( N( t)), t>0, which can be represented as random products. The last section is devoted to studying continued fractions of Cauchy random variables with a Poisson number of levels. We evaluate the exact distribution and derive the scale parameter in terms of ratios of Fibonacci numbers.
Nonequilibrium thermodynamics of restricted Boltzmann machines
Salazar, Domingos S. P.
2017-08-01
In this work, we analyze the nonequilibrium thermodynamics of a class of neural networks known as restricted Boltzmann machines (RBMs) in the context of unsupervised learning. We show how the network is described as a discrete Markov process and how the detailed balance condition and the Maxwell-Boltzmann equilibrium distribution are sufficient conditions for a complete thermodynamics description, including nonequilibrium fluctuation theorems. Numerical simulations in a fully trained RBM are performed and the heat exchange fluctuation theorem is verified with excellent agreement to the theory. We observe how the contrastive divergence functional, mostly used in unsupervised learning of RBMs, is closely related to nonequilibrium thermodynamic quantities. We also use the framework to interpret the estimation of the partition function of RBMs with the annealed importance sampling method from a thermodynamics standpoint. Finally, we argue that unsupervised learning of RBMs is equivalent to a work protocol in a system driven by the laws of thermodynamics in the absence of labeled data.
Lattice-Boltzmann simulations of droplet evaporation
Ledesma-Aguilar, Rodrigo
2014-09-04
© the Partner Organisations 2014. We study the utility and validity of lattice-Boltzmann (LB) simulations to explore droplet evaporation driven by a concentration gradient. Using a binary-fluid lattice-Boltzmann algorithm based on Cahn-Hilliard dynamics, we study the evaporation of planar films and 3D sessile droplets from smooth solid surfaces. Our results show that LB simulations accurately reproduce the classical regime of quasi-static dynamics. Beyond this limit, we show that the algorithm can be used to explore regimes where the evaporative and diffusive timescales are not widely separated, and to include the effect of boundaries of prescribed driving concentration. We illustrate the method by considering the evaporation of a droplet from a solid surface that is chemically patterned with hydrophilic and hydrophobic stripes. This journal is
A Nonlocal Poisson-Fermi Model for Ionic Solvent
Xie, Dexuan; Eisenberg, Bob; Scott, L Ridgway
2016-01-01
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-type kernel function. Moreover, the Fermi distribution is shown to be a set of optimal ionic concentration functions in the sense of minimizing an electrostatic potential free energy. Finally, numerical results are reported to show the difference between a Poisson-Fermi solution and a corresponding Poisson solution.
Nonlocal Poisson-Fermi model for ionic solvent.
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.
The Boltzmann equation in the difference formulation
Szoke, Abraham [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Brooks III, Eugene D. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
2015-05-06
First we recall the assumptions that are needed for the validity of the Boltzmann equation and for the validity of the compressible Euler equations. We then present the difference formulation of these equations and make a connection with the time-honored Chapman - Enskog expansion. We discuss the hydrodynamic limit and calculate the thermal conductivity of a monatomic gas, using a simplified approximation for the collision term. Our formulation is more consistent and simpler than the traditional derivation.
Boltzmann equations for neutrinos with flavor mixings
Yamada, Shoichi
2000-01-01
With a view of applications to the simulations of supernova explosion and proto neutron star cooling, we derive the Boltzmann equations for the neutrino transport with the flavor mixing based on the real time formalism of the nonequilibrium field theory and the gradient expansion of the Green function. The relativistic kinematics is properly taken into account. The advection terms are derived in the mean field approximation for the neutrino self-energy whiles the collision terms are obtained ...
Hybrid lattice Boltzmann method on overlapping grids.
Di Ilio, G; Chiappini, D; Ubertini, S; Bella, G; Succi, S
2017-01-01
In this work, a hybrid lattice Boltzmann method (HLBM) is proposed, where the standard lattice Boltzmann implementation based on the Bhatnagar-Gross-Krook (LBGK) approximation is combined together with an unstructured finite-volume lattice Boltzmann model. The method is constructed on an overlapping grid system, which allows the coexistence of a uniform lattice nodes spacing and a coordinate-free lattice structure. The natural adaptivity of the hybrid grid system makes the method particularly suitable to handle problems involving complex geometries. Moreover, the provided scheme ensures a high-accuracy solution near walls, given the capability of the unstructured submodel of achieving the desired level of refinement in a very flexible way. For these reasons, the HLBM represents a prospective tool for solving multiscale problems. The proposed method is here applied to the benchmark problem of a two-dimensional flow past a circular cylinder for a wide range of Reynolds numbers and its numerical performances are measured and compared with the standard LBGK ones.
Consistent lattice Boltzmann equations for phase transitions.
Siebert, D N; Philippi, P C; Mattila, K K
2014-11-01
Unlike conventional computational fluid dynamics methods, the lattice Boltzmann method (LBM) describes the dynamic behavior of fluids in a mesoscopic scale based on discrete forms of kinetic equations. In this scale, complex macroscopic phenomena like the formation and collapse of interfaces can be naturally described as related to source terms incorporated into the kinetic equations. In this context, a novel athermal lattice Boltzmann scheme for the simulation of phase transition is proposed. The continuous kinetic model obtained from the Liouville equation using the mean-field interaction force approach is shown to be consistent with diffuse interface model using the Helmholtz free energy. Density profiles, interface thickness, and surface tension are analytically derived for a plane liquid-vapor interface. A discrete form of the kinetic equation is then obtained by applying the quadrature method based on prescribed abscissas together with a third-order scheme for the discretization of the streaming or advection term in the Boltzmann equation. Spatial derivatives in the source terms are approximated with high-order schemes. The numerical validation of the method is performed by measuring the speed of sound as well as by retrieving the coexistence curve and the interface density profiles. The appearance of spurious currents near the interface is investigated. The simulations are performed with the equations of state of Van der Waals, Redlich-Kwong, Redlich-Kwong-Soave, Peng-Robinson, and Carnahan-Starling.
On the full Boltzmann equations for Leptogenesis
Garayoa, J; Pinto, T; Rius, N; Vives, O
2009-01-01
We consider the full Boltzmann equations for standard and soft leptogenesis, instead of the usual integrated Boltzmann equations which assume kinetic equilibrium for all species. Decays and inverse decays may be inefficient for thermalising the heavy-(s)neutrino distribution function, leading to significant deviations from kinetic equilibrium. We analyse the impact of using the full kinetic equations in the case of a previously generated lepton asymmetry, and find that the washout of this initial asymmetry due to the interactions of the right-handed neutrino is larger than when calculated via the integrated equations. We also solve the full Boltzmann equations for soft leptogenesis, where the lepton asymmetry induced by the soft SUSY-breaking terms in sneutrino decays is a purely thermal effect, since at T=0 the asymmetry in leptons cancels the one in sleptons. In this case, we obtain that in the weak washout regime (K ~< 1) the final lepton asymmetry can change up to a factor four with respect to previous...
On the full Boltzmann equations for leptogenesis
Garayoa, J.; Pastor, S.; Pinto, T.; Rius, N.; Vives, O., E-mail: garayoa@ific.uv.es, E-mail: pastor@ific.uv.es, E-mail: teguayco@gmail.com, E-mail: nuria@ific.uv.es, E-mail: vives@ific.uv.es [Depto. de Física Teórica and IFIC, Universidad de Valencia-CSIC, Edificio de Institutos de Paterna, Apt. 22085, 46071 Valencia (Spain)
2009-09-01
We consider the full Boltzmann equations for standard and soft leptogenesis, instead of the usual integrated Boltzmann equations which assume kinetic equilibrium for all species. Decays and inverse decays may be inefficient for thermalising the heavy-(s)neutrino distribution function, leading to significant deviations from kinetic equilibrium. We analyse the impact of using the full kinetic equations in the case of a previously generated lepton asymmetry, and find that the washout of this initial asymmetry due to the interactions of the right-handed neutrino is larger than when calculated via the integrated equations. We also solve the full Boltzmann equations for soft leptogenesis, where the lepton asymmetry induced by the soft SUSY-breaking terms in sneutrino decays is a purely thermal effect, since at T = 0 the asymmetry in leptons cancels the one in sleptons. In this case, we obtain that in the weak washout regime (K ∼< 1) the final lepton asymmetry can change up to a factor four with respect to previous estimates.
Convection in multiphase flows using Lattice Boltzmann methods
Biferale, L; Sbragaglia, M; Toschi, F
2011-01-01
We present high resolution numerical simulations of convection in multiphase flows (boiling) using a novel algorithm based on a Lattice Boltzmann method. We first validate the thermodynamical and kinematical properties of the algorithm. Then, we perform a series of 3d numerical simulations at changing the mean properties in the phase diagram and compare convection with and without phase coexistence at $Ra \\sim 10^7$. We show that in presence of nucleating bubbles non-Oberbeck Boussinesq effects develops, mean temperature profile becomes asymmetric, heat-transfer and heat-transfer fluctuations are enhanced. We also show that small-scale properties of velocity and temperature fields are strongly affected by the presence of buoyant bubble leading to high non-Gaussian profiles in the bulk.
On the fractal characterization of Paretian Poisson processes
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.
Compositions, Random Sums and Continued Random Fractions of Poisson and Fractional Poisson Processes
Orsingher, Enzo
2011-01-01
In this paper we consider the relation between random sums and compositions of different processes. In particular, for independent Poisson processes $N_\\alpha(t)$, $N_\\beta(t)$, $t>0$, we show that $N_\\alpha(N_\\beta(t)) \\overset{\\text{d}}{=} \\sum_{j=1}^{N_\\beta(t)} X_j$, where the $X_j$s are Poisson random variables. We present a series of similar cases, the most general of which is the one in which the outer process is Poisson and the inner one is a nonlinear fractional birth process. We highlight generalisations of these results where the external process is infinitely divisible. A section of the paper concerns compositions of the form $N_\\alpha(\\tau_k^\
Wang, Yahui; Yan, Liming; Ma, Yu
2017-06-01
Applications of the transient Boltzmann transport equation (BTE) have undergone much investigation, such as radiative heat transfer and neutron transport. This paper provides a lattice Boltzmann model to efficiently resolve the multidimensional transient BTE. For a higher angular resolution, enough transport directions are considered while the transient BTE in each direction is treated as a conservation law equation and solved independently. Both macroscopic equations recovered from a Chapman-Enskog expansion and simulated results of typical benchmark problems show not only the second-order accuracy but also the flexibility and applicability of the proposed lattice Boltzmann model. This approach may contribute a powerful technique for the parallel simulation of large-scale engineering and some alternative perspectives for solving the nonlinear transport problem further.
Analysis of overdispersed count data by mixtures of Poisson variables and Poisson processes.
Hougaard, P; Lee, M L; Whitmore, G A
1997-12-01
Count data often show overdispersion compared to the Poisson distribution. Overdispersion is typically modeled by a random effect for the mean, based on the gamma distribution, leading to the negative binomial distribution for the count. This paper considers a larger family of mixture distributions, including the inverse Gaussian mixture distribution. It is demonstrated that it gives a significantly better fit for a data set on the frequency of epileptic seizures. The same approach can be used to generate counting processes from Poisson processes, where the rate or the time is random. A random rate corresponds to variation between patients, whereas a random time corresponds to variation within patients.
Fujii, Y. [Japan National Oil Corp., Tokyo (Japan)
1998-04-01
This paper discusses the relationship between elastic wave velocities and physical properties of reservoir rocks. For sandstones, the elastic wave velocity decreases with increasing the porosity and the content of clay minerals. For rocks containing heavy oil, the P-wave velocity decreases with increasing the temperature. The P-wave velocity under dry condition is much more lower than that under water saturated condition. When there are a few percent of gas in pores against the water saturated condition, the P-wave velocity decreases rapidly. It is almost constant under the lower water saturation factor. The S-wave velocity is almost constant independent of the water saturation factor. Accordingly, the water saturation factor can not be estimated from the elastic wave velocity at the water saturation factor between 0% and 96%. The Poisson`s ratio also greatly decreases at the water saturation factor between 96% and 100%, but it is almost constant under the lower water saturation factor. The elastic wave velocity increases with increasing the pressure or increasing the depth. Since closure of cracks by pressure is inhibited due to high pore pressure, degree of increase in the elastic wave velocity is reduced. 14 refs., 6 figs.
Analogues of Euler and Poisson Summation Formulae
Vivek V Rane
2003-08-01
Euler–Maclaurin and Poisson analogues of the summations $\\sum_{a < n ≤ b}(n)f(n), \\sum_{a < n ≤ b}d(n) f(n), \\sum_{a < n ≤ b}d(n)(n) f(n)$ have been obtained in a unified manner, where (()) is a periodic complex sequence; () is the divisor function and () is a sufficiently smooth function on [, ]. We also state a generalised Abel's summation formula, generalised Euler's summation formula and Euler's summation formula in several variables.
The Poisson ratio of crystalline surfaces
Falcioni, Marco; Bowick, Mark; Guitter, Emmanuel; Thorleifsson, Gudmar
1996-01-01
A remarkable theoretical prediction for a crystalline (polymerized) surface is that its Poisson ratio (\\sigma) is negative. Using a large scale Monte Carlo simulation of a simple model of such surfaces we show that this is indeed true. The precise numerical value we find is (\\sigma \\simeq -0.32) on a (128^2) lattice at bending rigidity (kappa = 1.1). This is in excellent agreement with the prediction (\\sigma = -1/3) following from the self-consistent screening approximation of Le Doussal and ...
Poisson sigma models and deformation quantization
Cattaneo, A S; Cattaneo, Alberto S.; Felder, Giovanni
2001-01-01
This is a review aimed at a physics audience on the relation between Poisson sigma models on surfaces with boundary and deformation quantization. These models are topological open string theories. In the classical Hamiltonian approach, we describe the reduced phase space and its structures (symplectic groupoid), explaining in particular the classical origin of the non-commutativity of the string end-point coordinates. We also review the perturbative Lagrangian approach and its connection with Kontsevich's star product. Finally we comment on the relation between the two approaches.
Deterministic Thinning of Finite Poisson Processes
Angel, Omer; Soo, Terry
2009-01-01
Let Pi and Gamma be homogeneous Poisson point processes on a fixed set of finite volume. We prove a necessary and sufficient condition on the two intensities for the existence of a coupling of Pi and Gamma such that Gamma is a deterministic function of Pi, and all points of Gamma are points of Pi. The condition exhibits a surprising lack of monotonicity. However, in the limit of large intensities, the coupling exists if and only if the expected number of points is at least one greater in Pi than in Gamma.
Lou, James; Shih, Chun-Yu; Lee, Eric
2010-01-05
Diffusiophoresis in concentrated suspensions of spherical colloids with charge-regulated surface is investigated theoretically. The charge-regulated surface considered here is the generalization of conventional constant surface potential and constant surface charge density situations. Kuwabara's unit cell model is adopted to describe the system and a pseudospectral method based on Chebyshev polynomial is employed to solve the governing general electrokinetic equations. Excellent agreements with experimental data available in literature were obtained for the limiting case of constant surface potential and very dilute suspension. It is found, among other things, that in general the larger the number of dissociated functional groups on particle surface is, the higher the particle surface potential, hence the larger the magnitude of the particle mobility. The electric potential on particle surface depends on both the concentration of dissociated hydrogen ions and the concentration of electrolyte in the solution. The electric potential on particle surface turns out to be the dominant factor in the determination of the eventual particle diffusiophoretic mobility. Local maximum of diffusiophoretic mobility as a function of double layer thickness is observed. Its reason and influence is discussed. Corresponding behavior for the constant potential situation, however, may yield a monotonously increasing profile.
2012-01-01
The definition of a molecular surface which is physically sound and computationally efficient is a very interesting and long standing problem in the implicit solvent continuum modeling of biomolecular systems as well as in the molecular graphics field. In this work, two molecular surfaces are evaluated with respect to their suitability for electrostatic computation as alternatives to the widely used Connolly-Richards surface: the blobby surface, an implicit Gaussian atom centered surface, and...
Around Poisson--Mehler summation formula
Szabłowski, Paweł J
2011-01-01
We study some simple generalizations of the Poisson-Mehler summation formula (PM). In particular we exploit farther, the recently obtained equality {\\gamma}_{m,n}(x,y|t,q) = {\\gamma}_{0,0}(x,y|t,q)Q_{m,n}(x,y|t,q) where {\\gamma}_{m,n}(x,y|t,q) = \\Sigma_{i\\geq0}((t^{i})/([i]_{q}!))H_{i+n}(x|q)H_{m+i}(y|q), {H_{n}(x|q)}_{n\\geq-1} are the so called q-Hermite polynomials and {Q_{m,n}(x,y|t,q)}_{n,m\\geq0} are certain polynomials in x,y of order m+n being rational functions in t and q. We study properties of polynomials Q_{m,n}(x,y|t,q) expressing them with the help the so called Al-Salam--Chihara (ASC) polynomials and using them in expansion of the reciprocal of the right hand side of the Poisson-Mehler formula. We prove also some similar in nature equalities like e.g. the following \\Sigma_{i\\geq0}((t^{i})/([i]_{q}!))H_{n+i}(x|q) = H_{n}(x|t,q)\\Sigma_{i\\geq0}((t^{i})/([i]_{q}!))H_{i}(x|q), where H_{n}(x|t,q) is the so called big q-Hermite polynomial. We prove similar equalities involving big q-Hermite and ASC poly...
Renewal characterization of Markov modulated Poisson processes
Marcel F. Neuts
1989-01-01
Full Text Available A Markov Modulated Poisson Process (MMPP M(t defined on a Markov chain J(t is a pure jump process where jumps of M(t occur according to a Poisson process with intensity λi whenever the Markov chain J(t is in state i. M(t is called strongly renewal (SR if M(t is a renewal process for an arbitrary initial probability vector of J(t with full support on P={i:λi>0}. M(t is called weakly renewal (WR if there exists an initial probability vector of J(t such that the resulting MMPP is a renewal process. The purpose of this paper is to develop general characterization theorems for the class SR and some sufficiency theorems for the class WR in terms of the first passage times of the bivariate Markov chain [J(t,M(t]. Relevance to the lumpability of J(t is also studied.
Stoenescu, M.L.
1977-06-01
The terms in Boltzmann kinetic equation corresponding to elastic short range collisions, inelastic excitational collisions, coulomb interactions and electric field acceleration are evaluated numerically for a standard distribution function minimizing the computational volume by expressing the terms as linear combinations with recalculable coefficients, of the distribution function and its derivatives. The present forms are suitable for spatial distribution calculations.
PENERAPAN REGRESI BINOMIAL NEGATIF UNTUK MENGATASI OVERDISPERSI PADA REGRESI POISSON
PUTU SUSAN PRADAWATI
2013-09-01
Full Text Available Poisson regression was used to analyze the count data which Poisson distributed. Poisson regression analysis requires state equidispersion, in which the mean value of the response variable is equal to the value of the variance. However, there are deviations in which the value of the response variable variance is greater than the mean. This is called overdispersion. If overdispersion happens and Poisson Regression analysis is being used, then underestimated standard errors will be obtained. Negative Binomial Regression can handle overdispersion because it contains a dispersion parameter. From the simulation data which experienced overdispersion in the Poisson Regression model it was found that the Negative Binomial Regression was better than the Poisson Regression model.
PENERAPAN REGRESI BINOMIAL NEGATIF UNTUK MENGATASI OVERDISPERSI PADA REGRESI POISSON
PUTU SUSAN PRADAWATI
2013-09-01
Full Text Available Poisson regression was used to analyze the count data which Poisson distributed. Poisson regression analysis requires state equidispersion, in which the mean value of the response variable is equal to the value of the variance. However, there are deviations in which the value of the response variable variance is greater than the mean. This is called overdispersion. If overdispersion happens and Poisson Regression analysis is being used, then underestimated standard errors will be obtained. Negative Binomial Regression can handle overdispersion because it contains a dispersion parameter. From the simulation data which experienced overdispersion in the Poisson Regression model it was found that the Negative Binomial Regression was better than the Poisson Regression model.
Privacy-Preserving Restricted Boltzmann Machine
Li, Yu
2014-01-01
With the arrival of the big data era, it is predicted that distributed data mining will lead to an information technology revolution. To motivate different institutes to collaborate with each other, the crucial issue is to eliminate their concerns regarding data privacy. In this paper, we propose a privacy-preserving method for training a restricted boltzmann machine (RBM). The RBM can be got without revealing their private data to each other when using our privacy-preserving method. We provide a correctness and efficiency analysis of our algorithms. The comparative experiment shows that the accuracy is very close to the original RBM model. PMID:25101139
Lattice-Boltzmann-based Simulations of Diffusiophoresis
Castigliego, Joshua; Kreft Pearce, Jennifer
We present results from a lattice-Boltzmann-base Brownian Dynamics simulation on diffusiophoresis and the separation of particles within the system. A gradient in viscosity that simulates a concentration gradient in a dissolved polymer allows us to separate various types of particles by their deformability. As seen in previous experiments, simulated particles that have a higher deformability react differently to the polymer matrix than those with a lower deformability. Therefore, the particles can be separated from each other. This simulation, in particular, was intended to model an oceanic system where the particles of interest were zooplankton, phytoplankton and microplastics. The separation of plankton from the microplastics was achieved.
Celebrating Cercignani's conjecture for the Boltzmann equation
Desvillettes, Laurent; Villani, Cédric
2010-01-01
Cercignani's conjecture assumes a linear inequality between the entropy and entropy production functionals for Boltzmann's nonlinear integral operator in rarefied gas dynamics. Related to the field of logarithmic Sobolev inequalities and spectral gap inequalities, this issue has been at the core of the renewal of the mathematical theory of convergence to thermodynamical equilibrium for rarefied gases over the past decade. In this review paper, we survey the various positive and negative results which were obtained since the conjecture was proposed in the 1980s.
Poisson brackets of normal-ordered Wilson loops
Lee, C.-W. H.; Rajeev, S. G.
1999-04-01
We formulate Yang-Mills theory in terms of the large-N limit, viewed as a classical limit, of gauge-invariant dynamical variables, which are closely related to Wilson loops, via deformation quantization. We obtain a Poisson algebra of these dynamical variables corresponding to normal-ordered quantum (at a finite value of ℏ) operators. Comparing with a Poisson algebra one of us introduced in the past for Weyl-ordered quantum operators, we find, using ideas closely related to topological graph theory, that these two Poisson algebras are, roughly speaking, the same. More precisely speaking, there exists an invertible Poisson morphism between them.
Poisson process Fock space representation, chaos expansion and covariance inequalities
Last, Guenter
2009-01-01
We consider a Poisson process $\\eta$ on an arbitrary measurable space with an arbitrary sigma-finite intensity measure. We establish an explicit Fock space representation of square integrable functions of $\\eta$. As a consequence we identify explicitly, in terms of iterated difference operators, the integrands in the Wiener-Ito chaos expansion. We apply these results to extend well-known variance inequalities for homogeneous Poisson processes on the line to the general Poisson case. The Poincare inequality is a special case. Further applications are covariance identities for Poisson processes on (strictly) ordered spaces and Harris-FKG-inequalities for monotone functions of $\\eta$.
The fractional Poisson process and the inverse stable subordinator
Meerschaert, Mark M; Vellaisamy, P
2010-01-01
The fractional Poisson process is a renewal process with Mittag-Leffler waiting times. Its distributions solve a time-fractional analogue of the Kolmogorov forward equation for a Poisson process. This paper shows that a traditional Poisson process, with the time variable replaced by an independent inverse stable subordinator, is also a fractional Poisson process. This result unifies the two main approaches in the stochastic theory of time-fractional diffusion equations. The equivalence extends to a broad class of renewal processes that include models for tempered fractional diffusion, and distributed-order (e.g., ultraslow) fractional diffusion.
General relativistic Boltzmann equation, II: Manifestly covariant treatment
Debbasch, F.; van Leeuwen, W.A.
2009-01-01
In a preceding article we presented a general relativistic treatment of the derivation of the Boltzmann equation. The four-momenta occurring in this formalism were all on-shell four-momenta, verifying the mass-shell restriction p(2) = m(2)c(2). Due to this restriction, the resulting Boltzmann equati
Soluble Boltzmann equations for internal state and Maxwell models
Futcher, E.; Hoare, M.R.; Hendriks, E.M.; Ernst, M.H.
1980-01-01
We consider a class of scalar nonlinear Boltzmann equations describing the evolution of a microcanonical ensemble in which sub-systems exchange internal energy ‘randomly’ in binary interactions. In the continuous variable version these models can equally be interpreted as Boltzmann equations for Ma
Reciprocal Symmetric Boltzmann Function and Unified Boson-Fermion Statistics
2007-01-01
The differential equation for Boltzmann's function is replaced by the corresponding discrete finite difference equation. The difference equation is, then, symmetrized so that the equation remains invariant when step d is replaced by -d. The solutions of this equation come in Boson-Fermion pairs. Reciprocal symmetric Boltzmann's function, thus, unifies both Bosonic and Fermionic distributions.
Boltzmann's "H"-Theorem and the Assumption of Molecular Chaos
Boozer, A. D.
2011-01-01
We describe a simple dynamical model of a one-dimensional ideal gas and use computer simulations of the model to illustrate two fundamental results of kinetic theory: the Boltzmann transport equation and the Boltzmann "H"-theorem. Although the model is time-reversal invariant, both results predict that the behaviour of the gas is time-asymmetric.…
General relativistic Boltzmann equation, II: Manifestly covariant treatment
Debbasch, F.; van Leeuwen, W.A.
2009-01-01
In a preceding article we presented a general relativistic treatment of the derivation of the Boltzmann equation. The four-momenta occurring in this formalism were all on-shell four-momenta, verifying the mass-shell restriction p(2) = m(2)c(2). Due to this restriction, the resulting Boltzmann
Axisymmetric multiphase lattice Boltzmann method for generic equations of state
Reijers, Sten Arjen; Gelderblom, Hanneke; Toschi, F.
2016-01-01
We present an axisymmetric lattice Boltzmann model based on the Kupershtokh et al. multiphase model that is capable of solving liquid–gas density ratios up to 103. Appropriate source terms are added to the lattice Boltzmann evolution equation to fully recover the axisymmetric multiphase conservation
Distributional Monte Carlo Methods for the Boltzmann Equation
2013-03-01
become the first to possess non - Maxwellian distributions, and therefore become the only location where 112 collisions are required to be calculated... Maxwellian . . . . . . . . . . . . . . . . . 16 fMB Maxwell-Boltzmann Density . . . . . . . . . . . . . . . . . . . . . . . . 16 nMB Maxwell-Boltzmann...is equivalent to assuming that millions of actual particles all share the exact velocity vector. This assumption is non -physical in the sense that
Thermal equation of state for lattice Boltzmann gases
Ran Zheng
2009-01-01
The Galilean invaxiance and the induced thermo-hydrodynamics of the lattice Boltzmann Bhatnagar-Gross-Krook model axe proposed together with their rigorous theoretical background. From the viewpoint of group invariance,recovering the Galilean invariance for the isothermal lattice Boltzmann Bhatnagar-Gross-Krook equation (LBGKE) induces a new natural thermal-dynamical system, which is compatible with the elementary statistical thermodynamics.
Hot electrons in superlattices: quantum transport versus Boltzmann equation
Wacker, Andreas; Jauho, Antti-Pekka; Rott, S.;
1999-01-01
A self-consistent solution of the transport equation is presented for semiconductor superlattices within different approaches: (i) a full quantum transport model based on nonequilibrium Green functions, (ii) the semiclassical Boltzmann equation for electrons in a miniband, and (iii) Boltzmann...
Axisymmetric multiphase lattice Boltzmann method for generic equations of state
Reijers, S.A.; Gelderblom, H.; Toschi, F.
2016-01-01
We present an axisymmetric lattice Boltzmann model based on the Kupershtokh et al. multiphase model that is capable of solving liquid–gas density ratios up to 103. Appropriate source terms are added to the lattice Boltzmann evolution equation to fully recover the axisymmetric multiphase conservation
Surface reconstruction through poisson disk sampling.
Wenguang Hou
Full Text Available This paper intends to generate the approximate Voronoi diagram in the geodesic metric for some unbiased samples selected from original points. The mesh model of seeds is then constructed on basis of the Voronoi diagram. Rather than constructing the Voronoi diagram for all original points, the proposed strategy is to run around the obstacle that the geodesic distances among neighboring points are sensitive to nearest neighbor definition. It is obvious that the reconstructed model is the level of detail of original points. Hence, our main motivation is to deal with the redundant scattered points. In implementation, Poisson disk sampling is taken to select seeds and helps to produce the Voronoi diagram. Adaptive reconstructions can be achieved by slightly changing the uniform strategy in selecting seeds. Behaviors of this method are investigated and accuracy evaluations are done. Experimental results show the proposed method is reliable and effective.
Accuracy analysis of a spectral Poisson solver
Rambaldi, S. [Dipartimento di Fisica Universita di Bologna and INFN, Bologna, Via Irnerio 46, 40126 (Italy)]. E-mail: rambaldi@bo.infn.it; Turchetti, G. [Dipartimento di Fisica Universita di Bologna and INFN, Bologna, Via Irnerio 46, 40126 (Italy); Benedetti, C. [Dipartimento di Fisica Universita di Bologna and INFN, Bologna, Via Irnerio 46, 40126 (Italy); Mattioli, F. [Dipartimento di Fisica Universita di Bologna, Bologna, Via Irnerio 46, 40126 (Italy); Franchi, A. [GSI, Darmstadt, Planckstr. 1, 64291 (Germany)
2006-06-01
We solve Poisson's equation in d=2,3 space dimensions by using a spectral method based on Fourier decomposition. The choice of the basis implies that Dirichlet boundary conditions on a box are satisfied. A Green's function-based procedure allows us to impose Dirichlet conditions on any smooth closed boundary, by doubling the computational complexity. The error introduced by the spectral truncation and the discretization of the charge distribution is evaluated by comparison with the exact solution, known in the case of elliptical symmetry. To this end boundary conditions on an equipotential ellipse (ellipsoid) are imposed on the numerical solution. Scaling laws for the error dependence on the number K of Fourier components for each space dimension and the number N of point charges used to simulate the charge distribution are presented and tested. A procedure to increase the accuracy of the method in the beam core region is briefly outlined.
Classical covariant Poisson structures and Deformation Quantization
Berra-Montiel, Jasel; Palacios-García, César D
2014-01-01
Starting with the well-defined product of quantum fields at two spacetime points, we explore an associated Poisson structure for classical field theories within the deformation quantization formalism. We realize that the induced star-product is naturally related to the standard Moyal product through the causal Green functions connecting points in the space of classical solutions to the equations of motion. Our results resemble the Peierls-DeWitt bracket analyzed in the multisymplectic context. Once our star-product is defined we are able to apply the Wigner-Weyl map in order to introduce a generalized version of Wick's theorem. Finally, we include a couple of examples to explicitly test our method: the real scalar field and the bosonic string. For both models we have encountered generalizations of the creation/annihilation relations, and also a generalization of the Virasoro algebra in the bosonic string case.
High order Poisson Solver for unbounded flows
Hejlesen, Mads Mølholm; Rasmussen, Johannes Tophøj; Chatelain, Philippe
2015-01-01
as regularisation we document an increased convergence rate up to tenth order. The method however, can easily be extended well beyond the tenth order. To show the full extend of the method we present the special case of a spectrally ideal regularisation of the velocity formulated integration kernel, which achieves......This paper presents a high order method for solving the unbounded Poisson equation on a regular mesh using a Green’s function solution. The high order convergence was achieved by formulating mollified integration kernels, that were derived from a filter regularisation of the solution field...... or by performing the differentiation as a multiplication of the Fourier coefficients. In this way, differential operators such as the divergence or curl of the solution field could be solved to the same high order convergence without additional computational effort. The method was applied and validated using...
Multireflection boundary conditions for lattice Boltzmann models.
Ginzburg, Irina; d'Humières, Dominique
2003-12-01
We present a general framework for several previously introduced boundary conditions for lattice Boltzmann models, such as the bounce-back rule and the linear and quadratic interpolations. The objectives are twofold: first to give theoretical tools to study the existing link-type boundary conditions and their corresponding accuracy; second to design boundary conditions for general flows which are third-order kinetic accurate. Using these new boundary conditions, Couette and Poiseuille flows are exact solutions of the lattice Boltzmann models for a Reynolds number Re=0 (Stokes limit) for arbitrary inclination with the lattice directions. Numerical comparisons are given for Stokes flows in periodic arrays of spheres and cylinders, linear periodic array of cylinders between moving plates, and for Navier-Stokes flows in periodic arrays of cylinders for Re<200. These results show a significant improvement of the overall accuracy when using the linear interpolations instead of the bounce-back reflection (up to an order of magnitude on the hydrodynamics fields). Further improvement is achieved with the new multireflection boundary conditions, reaching a level of accuracy close to the quasianalytical reference solutions, even for rather modest grid resolutions and few points in the narrowest channels. More important, the pressure and velocity fields in the vicinity of the obstacles are much smoother with multireflection than with the other boundary conditions. Finally the good stability of these schemes is highlighted by some simulations of moving obstacles: a cylinder between flat walls and a sphere in a cylinder.
Entropic Lattice Boltzmann Methods for Fluid Mechanics
Chikatamarla, Shyam; Boesch, Fabian; Sichau, David; Karlin, Ilya
2013-11-01
With its roots in statistical mechanics and kinetic theory, the lattice Boltzmann method (LBM) is a paradigm-changing innovation, offering for the first time an intrinsically parallel CFD algorithm. Over the past two decades, LBM has achieved numerous results in the field of CFD and is now in a position to challenge state-of-the art CFD techniques. Our major restyling of LBM resulted in an unconditionally stable entropic LBM which restored Second Law (Boltzmann H theorem) in the LBM kinetics and thus enabled affordable direct simulations of fluid turbulence. We review here recent advances in ELBM as a practical, modeling-free tool for simulation of turbulent flows in complex geometries. We shall present recent simulations including turbulent channel flow, flow past a circular cylinder, knotted vortex tubes, and flow past a surface mounted cube. ELBM listed all admissible lattices supporting a discrete entropy function and has classified them in hierarchically increasing order of accuracy. Applications of these higher-order lattices to simulations of turbulence and thermal flows shall also be presented. This work was supported CSCS grant s437.
Immersed boundary lattice Boltzmann model based on multiple relaxation times.
Lu, Jianhua; Han, Haifeng; Shi, Baochang; Guo, Zhaoli
2012-01-01
As an alterative version of the lattice Boltzmann models, the multiple relaxation time (MRT) lattice Boltzmann model introduces much less numerical boundary slip than the single relaxation time (SRT) lattice Boltzmann model if some special relationship between the relaxation time parameters is chosen. On the other hand, most current versions of the immersed boundary lattice Boltzmann method, which was first introduced by Feng and improved by many other authors, suffer from numerical boundary slip as has been investigated by Le and Zhang. To reduce such a numerical boundary slip, an immerse boundary lattice Boltzmann model based on multiple relaxation times is proposed in this paper. A special formula is given between two relaxation time parameters in the model. A rigorous analysis and the numerical experiments carried out show that the numerical boundary slip reduces dramatically by using the present model compared to the single-relaxation-time-based model.
Boltzmann equations for a binary one-dimensional ideal gas.
Boozer, A D
2011-09-01
We consider a time-reversal invariant dynamical model of a binary ideal gas of N molecules in one spatial dimension. By making time-asymmetric assumptions about the behavior of the gas, we derive Boltzmann and anti-Boltzmann equations that describe the evolution of the single-molecule velocity distribution functions for an ensemble of such systems. We show that for a special class of initial states of the ensemble one can obtain an exact expression for the N-molecule velocity distribution function, and we use this expression to rigorously prove that the time-asymmetric assumptions needed to derive the Boltzmann and anti-Boltzmann equations hold in the limit of large N. Our results clarify some subtle issues regarding the origin of the time asymmetry of Boltzmann's H theorem.
Steady-State Anderson Accelerated Coupling of Lattice Boltzmann and Navier–Stokes Solvers
Atanasov, Atanas
2016-10-17
We present an Anderson acceleration-based approach to spatially couple three-dimensional Lattice Boltzmann and Navier–Stokes (LBNS) flow simulations. This allows to locally exploit the computational features of both fluid flow solver approaches to the fullest extent and yields enhanced control to match the LB and NS degrees of freedom within the LBNS overlap layer. Designed for parallel Schwarz coupling, the Anderson acceleration allows for the simultaneous execution of both Lattice Boltzmann and Navier–Stokes solver. We detail our coupling methodology, validate it, and study convergence and accuracy of the Anderson accelerated coupling, considering three steady-state scenarios: plane channel flow, flow around a sphere and channel flow across a porous structure. We find that the Anderson accelerated coupling yields a speed-up (in terms of iteration steps) of up to 40% in the considered scenarios, compared to strictly sequential Schwarz coupling.
Premnath, Kannan N; Banerjee, Sanjoy
2008-01-01
Several applications exist in which lattice Boltzmann methods (LBM) are used to compute stationary states of fluid motions, particularly those driven or modulated by external forces. Standard LBM, being explicit time-marching in nature, requires a long time to attain steady state convergence, particularly at low Mach numbers due to the disparity in characteristic speeds of propagation of different quantities. In this paper, we present a preconditioned generalized lattice Boltzmann equation (GLBE) with forcing term to accelerate steady state convergence to flows driven by external forces. The use of multiple relaxation times in the GLBE allows enhancement of the numerical stability. Particular focus is given in preconditioning external forces, which can be spatially and temporally dependent. In particular, correct forms of moment-projections of source/forcing terms are derived such that they recover preconditioned Navier-Stokes equations with non-uniform external forces. As an illustration, we solve an extende...
Derivation of relativistic wave equation from the Poisson process
Tomoshige Kudo; Ichiro Ohba
2002-08-01
A Poisson process is one of the fundamental descriptions for relativistic particles: both fermions and bosons. A generalized linear photon wave equation in dispersive and homogeneous medium with dissipation is derived using the formulation of the Poisson process. This formulation provides a possible interpretation of the passage time of a photon moving in the medium, which never exceeds the speed of light in vacuum.
Canonical derivation of the Vlasov-Coulomb noncanonical Poisson structure
Kaufman, A.N.; Dewar, R.L.
1983-09-01
Starting from a Lagrangian formulation of the Vlasov-Coulomb system, canonical methods are used to define a Poisson structure for this system. Successive changes of representation then lead systematically to the noncanonical Lie-Poisson structure for functionals of the Vlasov distribution.
Deformations of log-Lagrangian submanifolds of Poisson manifolds
2013-01-01
We consider Lagrangian-like submanifolds in certain even-dimensional 'symplectic-like' Poisson manifolds. We show, under suitable transversality hypotheses, that the pair consisting of the ambient Poisson manifold and the submanifold has unobstructed deformations and that the deformations automatically preserve the Lagrangian-like property.
REGULARITY OF POISSON EQUATION IN SOME LOGARITHMIC SPACE
Jia Huilian; Li Dongsheng; Wang Lihe
2007-01-01
In this note, the regularity of Poisson equation -△u = f with f lying in logarithmic function space Lp(LogL)a(Ω)(1＜p ＜∞, a ∈ R) is studied. The result of the note generalizes the W2,p estimate of Poisson equation in Lp(Ω).
Topology Optimized Architectures with Programmable Poisson's Ratio over Large Deformations
Clausen, Anders; Wang, Fengwen; Jensen, Jakob Søndergaard
2015-01-01
Topology optimized architectures are designed and printed with programmable Poisson's ratios ranging from -0.8 to 0.8 over large deformations of 20% or more.......Topology optimized architectures are designed and printed with programmable Poisson's ratios ranging from -0.8 to 0.8 over large deformations of 20% or more....
Rate-optimal Bayesian intensity smoothing for inhomogeneous Poisson processes
E. Belitser; P. Serra; H. van Zanten
2015-01-01
We apply nonparametric Bayesian methods to study the problem of estimating the intensity function of an inhomogeneous Poisson process. To motivate our results we start by analyzing count data coming from a call center which we model as a Poisson process. This analysis is carried out using a certain
The Survival Probability in Generalized Poisson Risk Model
GONGRi-zhao
2003-01-01
In this paper we generalize the aggregated premium income process from a constant rate process to a poisson process for the classical compound Poinsson risk model,then for the generalized model and the classical compound poisson risk model ,we respectively get its survival probability in finite time period in case of exponential claim amounts.
Poisson-Lie T-Duality and Bianchi Type Algebras
Jafarizadeh, M A
1999-01-01
All Bianchi bialgebras have been obtained. By introducing a non-degenerate adjoint invariant inner product over these bialgebras the associated Drinfeld doubles have been constructed, then by calculating the coupling matrices for these bialgebras several \\sigma-models with Poisson-Lie symmetry have been obtained. Two simple examples as prototypes of Poisson-Lie dual models have been given.
Deformation mechanisms in negative Poisson's ratio materials - Structural aspects
Lakes, R.
1991-01-01
Poisson's ratio in materials is governed by the following aspects of the microstructure: the presence of rotational degrees of freedom, non-affine deformation kinematics, or anisotropic structure. Several structural models are examined. The non-affine kinematics are seen to be essential for the production of negative Poisson's ratios for isotropic materials containing central force linkages of positive stiffness. Non-central forces combined with pre-load can also give rise to a negative Poisson's ratio in isotropic materials. A chiral microstructure with non-central force interaction or non-affine deformation can also exhibit a negative Poisson's ratio. Toughness and damage resistance in these materials may be affected by the Poisson's ratio itself, as well as by generalized continuum aspects associated with the microstructure.
Boltzmann babies in the proper time measure
Bousso, Raphael; Bousso, Raphael; Freivogel, Ben; Yang, I-Sheng
2007-12-20
After commenting briefly on the role of the typicality assumption in science, we advocate a phenomenological approach to the cosmological measure problem. Like any other theory, a measure should be simple, general, well defined, and consistent with observation. This allows us to proceed by elimination. As an example, we consider the proper time cutoff on a geodesic congruence. It predicts that typical observers are quantum fluctuations in the early universe, or Boltzmann babies. We sharpen this well-known youngness problem by taking into account the expansion and open spatial geometry of pocket universes. Moreover, we relate the youngness problem directly to the probability distribution for observables, such as the temperature of the cosmic background radiation. We consider a number of modifications of the proper time measure, but find none that would make it compatible with observation.
Lattice Boltzmann Model for Numerical Relativity
Ilseven, E
2015-01-01
In the Bona-Masso formulation, Einstein equations are written as a set of flux conservative first order hyperbolic equations that resemble fluid dynamics equations. Based on this formulation, we construct a lattice Boltzmann model for Numerical Relativity. Our model is validated with well-established tests, showing good agreement with analytical solutions. Furthermore, we show that by increasing the relaxation time, we gain stability at the cost of losing accuracy, and by decreasing the lattice spacings while keeping a constant numerical diffusivity, the accuracy and stability of our simulations improves. Finally, in order to show the potential of our approach a linear scaling law for parallelisation with respect to number of CPU cores is demonstrated. Our model represents the first step in using lattice kinetic theory to solve gravitational problems.
Lattice Boltzmann model with nearly constant density.
Fang, Hai-ping; Wan, Rong-zheng; Lin, Zhi-fang
2002-09-01
An improved lattice Boltzmann model is developed to simulate fluid flow with nearly constant fluid density. The ingredient is to incorporate an extra relaxation for fluid density, which is realized by introducing a feedback equation in the equilibrium distribution functions. The pressure is dominated by the moving particles at a node, while the fluid density is kept nearly constant and explicit mass conservation is retained as well. Numerical simulation based on the present model for the (steady) plane Poiseuille flow and the (unsteady) two-dimensional Womersley flow shows a great improvement in simulation results over the previous models. In particular, the density fluctuation has been reduced effectively while achieving a relatively large pressure gradient.
Lattice Boltzmann modelling of intrinsic permeability
Li, Jun; Wu, Lei; Zhang, Yonghao
2016-01-01
Lattice Boltzmann method (LBM) has been applied to predict flow properties of porous media including intrinsic permeability, where it is implicitly assumed that the LBM is equivalent to the incompressible (or near incompressible) Navier-Stokes equation. However, in LBM simulations, high-order moments, which are completely neglected in the Navier-Stokes equation, are still available through particle distribution functions. To ensure that the LBM simulation is correctly working at the Navier-Stokes hydrodynamic level, the high-order moments have to be negligible. This requires that the Knudsen number (Kn) is small so that rarefaction effect can be ignored. In this technical note, we elaborate this issue in LBM modelling of porous media flows, which is particularly important for gas flows in ultra-tight media.
The Lattice Boltzmann method principles and practice
Krüger, Timm; Kuzmin, Alexandr; Shardt, Orest; Silva, Goncalo; Viggen, Erlend Magnus
2017-01-01
This book is an introduction to the theory, practice, and implementation of the Lattice Boltzmann (LB) method, a powerful computational fluid dynamics method that is steadily gaining attention due to its simplicity, scalability, extensibility, and simple handling of complex geometries. The book contains chapters on the method's background, fundamental theory, advanced extensions, and implementation. To aid beginners, the most essential paragraphs in each chapter are highlighted, and the introductory chapters on various LB topics are front-loaded with special "in a nutshell" sections that condense the chapter's most important practical results. Together, these sections can be used to quickly get up and running with the method. Exercises are integrated throughout the text, and frequently asked questions about the method are dealt with in a special section at the beginning. In the book itself and through its web page, readers can find example codes showing how the LB method can be implemented efficiently on a va...
A lattice Boltzmann model for adsorption breakthrough
Agarwal, Saurabh; Verma, Nishith [Indian Institute of Technology Kanpur, Department of Chemical Engineering, Kanpur (India); Mewes, Dieter [Universitat Hannover, Institut fur Verfahrenstechnik, Hannover (Germany)
2005-07-01
A lattice Boltzmann model is developed to simulate the one-dimensional (1D) unsteady state concentration profiles, including breakthrough curves, in a fixed tubular bed of non-porous adsorbent particles. The lattice model solves the 1D time dependent convection-diffusion-reaction equation for an ideal binary gaseous mixture, with solute concentrations at parts per million levels. The model developed in this study is also able to explain the experimental adsorption/desorption data of organic vapours (toluene) on silica gel under varying conditions of temperature, concentrations and flowrates. Additionally, the programming code written for simulating the adsorption breakthrough is modified with minimum changes to successfully simulate a few flow problems, such as Poiseuille flow, Couette flow, and axial dispersion in a tube. The present study provides an alternative numerical approach to solving such types of mass transfer related problems. (orig.)
Ordinal Boltzmann Machines for Collaborative Filtering
Truyen, Tran The; Venkatesh, Svetha
2012-01-01
Collaborative filtering is an effective recommendation technique wherein the preference of an individual can potentially be predicted based on preferences of other members. Early algorithms often relied on the strong locality in the preference data, that is, it is enough to predict preference of a user on a particular item based on a small subset of other users with similar tastes or of other items with similar properties. More recently, dimensionality reduction techniques have proved to be equally competitive, and these are based on the co-occurrence patterns rather than locality. This paper explores and extends a probabilistic model known as Boltzmann Machine for collaborative filtering tasks. It seamlessly integrates both the similarity and co-occurrence in a principled manner. In particular, we study parameterisation options to deal with the ordinal nature of the preferences, and propose a joint modelling of both the user-based and item-based processes. Experiments on moderate and large-scale movie recomm...
Lattice Boltzmann model for numerical relativity.
Ilseven, E; Mendoza, M
2016-02-01
In the Z4 formulation, Einstein equations are written as a set of flux conservative first-order hyperbolic equations that resemble fluid dynamics equations. Based on this formulation, we construct a lattice Boltzmann model for numerical relativity and validate it with well-established tests, also known as "apples with apples." Furthermore, we find that by increasing the relaxation time, we gain stability at the cost of losing accuracy, and by decreasing the lattice spacings while keeping a constant numerical diffusivity, the accuracy and stability of our simulations improve. Finally, in order to show the potential of our approach, a linear scaling law for parallelization with respect to number of CPU cores is demonstrated. Our model represents the first step in using lattice kinetic theory to solve gravitational problems.
Lattice Boltzmann model for resistive relativistic magnetohydrodynamics
Mohseni, F; Succi, S; Herrmann, H J
2015-01-01
In this paper, we develop a lattice Boltzmann model for relativistic magnetohydrodynamics (MHD). Even though the model is derived for resistive MHD, it is shown that it is numerically robust even in the high conductivity (ideal MHD) limit. In order to validate the numerical method, test simulations are carried out for both ideal and resistive limits, namely the propagation of Alfv\\'en waves in the ideal MHD and the evolution of current sheets in the resistive regime, where very good agreement is observed comparing to the analytical results. Additionally, two-dimensional magnetic reconnection driven by Kelvin-Helmholtz instability is studied and the effects of different parameters on the reconnection rate are investigated. It is shown that the density ratio has negligible effect on the magnetic reconnection rate, while an increase in shear velocity decreases the reconnection rate. Additionally, it is found that the reconnection rate is proportional to $\\sigma^{-\\frac{1}{2}}$, $\\sigma$ being the conductivity, w...
Training Restricted Boltzmann Machines on Word Observations
Dahl, George E; Larochelle, Hugo
2012-01-01
The restricted Boltzmann machine (RBM) is a flexible tool for modeling complex data, however there have been significant computational difficulties in using RBMs to model high-dimensional multinomial observations. In natural language processing applications, words are naturally modeled by K-ary discrete distributions, where K is determined by the vocabulary size and can easily be in the hundred thousands. The conventional approach to training RBMs on word observations is limited because it requires sampling the states of K-way softmax visible units during block Gibbs updates, an operation that takes time linear in K. In this work, we address this issue by employing a more general class of Markov chain Monte Carlo operators on the visible units, yielding updates with computational complexity independent of K. We demonstrate the success of our approach by training RBMs on hundreds of millions of word n-grams using larger vocabularies than previously feasible with RBMs and using the learned features to improve p...
Lattice Boltzmann modeling of water entry problems
Zarghami, A.; Falcucci, G.; Jannelli, E.; Succi, S.; Porfiri, M.; Ubertini, S.
2014-12-01
This paper deals with the simulation of water entry problems using the lattice Boltzmann method (LBM). The dynamics of the free surface is treated through the mass and momentum fluxes across the interface cells. A bounce-back boundary condition is utilized to model the contact between the fluid and the moving object. The method is implemented for the analysis of a two-dimensional flow physics produced by a symmetric wedge entering vertically a weakly-compressible fluid at a constant velocity. The method is used to predict the wetted length, the height of water pile-up, the pressure distribution and the overall force on the wedge. The accuracy of the numerical results is demonstrated through comparisons with data reported in the literature.
Classification of Sets using Restricted Boltzmann Machines
Louradour, Jérôme
2011-01-01
We consider the problem of classification when inputs correspond to sets of vectors. This setting occurs in many problems such as the classification of pieces of mail containing several pages, of web sites with several sections or of images that have been pre-segmented into smaller regions. We propose generalizations of the restricted Boltzmann machine (RBM) that are appropriate in this context and explore how to incorporate different assumptions about the relationship between the input sets and the target class within the RBM. In experiments on standard multiple-instance learning datasets, we demonstrate the competitiveness of approaches based on RBMs and apply the proposed variants to the problem of incoming mail classification.
Flux Limiter Lattice Boltzmann for Compressible Flows
陈峰; 许爱国; 张广财; 李英骏
2011-01-01
In this paper, a new flux limiter scheme with the splitting technique is successfully incorporated into a multiple-relaxation-time lattice Boltzmann （LB） model for shacked compressible flows. The proposed flux limiter scheme is efficient in decreasing the artificial oscillations and numerical diffusion around the interface. Due to the kinetic nature, some interface problems being difficult to handle at the macroscopic level can be modeled more naturally through the LB method. Numerical simulations for the Richtmyer-Meshkov instability show that with the new model the computed interfaces are smoother and more consistent with physical analysis. The growth rates of bubble and spike present a satisfying agreement with the theoretical predictions and other numerical simulations.
Accurate deterministic solutions for the classic Boltzmann shock profile
Yue, Yubei
The Boltzmann equation or Boltzmann transport equation is a classical kinetic equation devised by Ludwig Boltzmann in 1872. It is regarded as a fundamental law in rarefied gas dynamics. Rather than using macroscopic quantities such as density, temperature, and pressure to describe the underlying physics, the Boltzmann equation uses a distribution function in phase space to describe the physical system, and all the macroscopic quantities are weighted averages of the distribution function. The information contained in the Boltzmann equation is surprisingly rich, and the Euler and Navier-Stokes equations of fluid dynamics can be derived from it using series expansions. Moreover, the Boltzmann equation can reach regimes far from the capabilities of fluid dynamical equations, such as the realm of rarefied gases---the topic of this thesis. Although the Boltzmann equation is very powerful, it is extremely difficult to solve in most situations. Thus the only hope is to solve it numerically. But soon one finds that even a numerical simulation of the equation is extremely difficult, due to both the complex and high-dimensional integral in the collision operator, and the hyperbolic phase-space advection terms. For this reason, until few years ago most numerical simulations had to rely on Monte Carlo techniques. In this thesis I will present a new and robust numerical scheme to compute direct deterministic solutions of the Boltzmann equation, and I will use it to explore some classical gas-dynamical problems. In particular, I will study in detail one of the most famous and intrinsically nonlinear problems in rarefied gas dynamics, namely the accurate determination of the Boltzmann shock profile for a gas of hard spheres.
Baccelli, Francois
2011-01-01
We consider a queue where the server is the Euclidean space, and the customers are random closed sets (RACS) of the Euclidean space. These RACS arrive according to a Poisson rain and each of them has a random service time (in the case of hail falling on the Euclidean plane, this is the height of the hailstone, whereas the RACS is its footprint). The Euclidean space serves customers at speed 1. The service discipline is a hard exclusion rule: no two intersecting RACS can be served simultaneously and service is in the First In First Out order: only the hailstones in contact with the ground melt at speed 1, whereas the other ones are queued; a tagged RACS waits until all RACS arrived before it and intersecting it have fully melted before starting its own melting. We give the evolution equations for this queue. We prove that it is stable for a sufficiently small arrival intensity, provided the typical diameter of the RACS and the typical service time have finite exponential moments. We also discuss the percolatio...
Causal Poisson bracket via deformation quantization
Berra-Montiel, Jasel; Molgado, Alberto; Palacios-García, César D.
2016-06-01
Starting with the well-defined product of quantum fields at two spacetime points, we explore an associated Poisson structure for classical field theories within the deformation quantization formalism. We realize that the induced star-product is naturally related to the standard Moyal product through an appropriate causal Green’s functions connecting points in the space of classical solutions to the equations of motion. Our results resemble the Peierls-DeWitt bracket that has been analyzed in the multisymplectic context. Once our star-product is defined, we are able to apply the Wigner-Weyl map in order to introduce a generalized version of Wick’s theorem. Finally, we include some examples to explicitly test our method: the real scalar field, the bosonic string and a physically motivated nonlinear particle model. For the field theoretic models, we have encountered causal generalizations of the creation/annihilation relations, and also a causal generalization of the Virasoro algebra for the bosonic string. For the nonlinear particle case, we use the approximate solution in terms of the Green’s function, in order to construct a well-behaved causal bracket.
Vlasov-Poisson in 1D: waterbags
Colombi, Stéphane
2014-01-01
We revisit in one dimension the waterbag method to solve numerically Vlasov-Poisson equations. In this approach, the phase-space distribution function $f(x,v)$ is initially sampled by an ensemble of patches, the waterbags, where $f$ is assumed to be constant. As a consequence of Liouville theorem it is only needed to follow the evolution of the border of these waterbags, which can be done by employing an orientated, self-adaptive polygon tracing isocontours of $f$. This method, which is entropy conserving in essence, is very accurate and can trace very well non linear instabilities as illustrated by specific examples. As an application of the method, we generate an ensemble of single waterbag simulations with decreasing thickness, to perform a convergence study to the cold case. Our measurements show that the system relaxes to a steady state where the gravitational potential profile is a power-law of slowly varying index $\\beta$, with $\\beta$ close to $3/2$ as found in the literature. However, detailed analys...
Integer lattice dynamics for Vlasov-Poisson
Mocz, Philip; Succi, Sauro
2017-03-01
We revisit the integer lattice (IL) method to numerically solve the Vlasov-Poisson equations, and show that a slight variant of the method is a very easy, viable, and efficient numerical approach to study the dynamics of self-gravitating, collisionless systems. The distribution function lives in a discretized lattice phase-space, and each time-step in the simulation corresponds to a simple permutation of the lattice sites. Hence, the method is Lagrangian, conservative, and fully time-reversible. IL complements other existing methods, such as N-body/particle mesh (computationally efficient, but affected by Monte Carlo sampling noise and two-body relaxation) and finite volume (FV) direct integration schemes (expensive, accurate but diffusive). We also present improvements to the FV scheme, using a moving-mesh approach inspired by IL, to reduce numerical diffusion and the time-step criterion. Being a direct integration scheme like FV, IL is memory limited (memory requirement for a full 3D problem scales as N6, where N is the resolution per linear phase-space dimension). However, we describe a new technique for achieving N4 scaling. The method offers promise for investigating the full 6D phase-space of collisionless systems of stars and dark matter.
Integer Lattice Dynamics for Vlasov-Poisson
Mocz, Philip
2016-01-01
We revisit the integer lattice (IL) method to numerically solve the Vlasov-Poisson equations, and show that a slight variant of the method is a very easy, viable, and efficient numerical approach to study the dynamics of self-gravitating, collisionless systems. The distribution function lives in a discretized lattice phase-space, and each time-step in the simulation corresponds to a simple permutation of the lattice sites. Hence, the method is Lagrangian, conservative, and fully time-reversible. IL complements other existing methods, such as N-body/particle mesh (computationally efficient, but affected by Monte-Carlo sampling noise and two-body relaxation) and finite volume (FV) direct integration schemes (expensive, accurate but diffusive). We also present improvements to the FV scheme, using a moving mesh approach inspired by IL, to reduce numerical diffusion and the time-step criterion. Being a direct integration scheme like FV, IL is memory limited (memory requirement for a full 3D problem scales as N^6, ...
Poisson structures on affine spaces and flag varieties. I. Matrix affine Poisson space
K. A. Brown; Goodearl, K. R.; Yakimov, M
2006-01-01
The standard Poisson structure on the rectangular matrix variety Mm,n(C) is\\ud investigated, via the orbits of symplectic leaves under the action of the maximal torus T ⊂\\ud GLm+n(C). These orbits, finite in number, are shown to be smooth irreducible locally closed\\ud subvarieties of Mm,n(C), isomorphic to intersections of dual Schubert cells in the full flag\\ud variety of GLm+n(C). Three different presentations of the T-orbits of symplectic leaves in\\ud Mm,n(C) are obtained – (a) as pu...
On classification of discrete, scalar-valued Poisson Brackets
Parodi, Emanuele
2011-01-01
We address the problem of classifying discrete differential-geometric Poisson brackets (dDGPBs) of any fixed order on target space of dimension 1. It is proved that these Poisson brackets (PBs) are in one-to-one correspondence with the intersection points of certain projective hypersurfaces. In addition, they can be reduced to cubic PB of standard Volterra lattice by discrete Miura-type transformations. Finally, improving a consolidation lattice procedure, we obtain new families of non-degenerate, vector-valued and first order dDGPBs, which can be considered in the framework of admissible Lie-Poisson group theory.
Absolute regularity and ergodicity of Poisson count processes
Neumann, Michael H
2012-01-01
We consider a class of observation-driven Poisson count processes where the current value of the accompanying intensity process depends on previous values of both processes. We show under a contractive condition that the bivariate process has a unique stationary distribution and that a stationary version of the count process is absolutely regular. Moreover, since the intensities can be written as measurable functionals of the count variables, we conclude that the bivariate process is ergodic. As an important application of these results, we show how a test method previously used in the case of independent Poisson data can be used in the case of Poisson count processes.
Algebraic structure and Poisson's theory of mechanico-electrical systems
Liu Hong-Ji; Tang Yi-Fa; Fu Jing-Li
2006-01-01
The algebraic structure and Poisson's integral theory of mechanico-electrical systems are studied.The Hamilton canonical equations and generalized Hamilton canonical equations and their the contravariant algebraic forms for mechanico-electrical systems are obtained.The Lie algebraic structure and the Poisson's integral theory of Lagrange mechanico-electrical systems are derived.The Lie algebraic structure admitted and Poisson's integral theory of the Lagrange-Maxwell mechanico-electrical systems are presented.Two examples are presented to illustrate these results.
Intertime jump statistics of state-dependent Poisson processes.
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.
Intertime jump statistics of state-dependent Poisson processes
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.
Noise source identification with the lattice Boltzmann method.
Vergnault, Etienne; Malaspinas, Orestis; Sagaut, Pierre
2013-03-01
In this paper the sound source identification problem is addressed with the use of the lattice Boltzmann method. To this aim, a time-reversed problem coupled to a complex differentiation method is used. In order to circumvent the inherent instability of the time-reversed lattice Boltzmann scheme, a method based on a split of the lattice Boltzmann equation into a mean and a perturbation component is used. Lattice Boltzmann method formulation around an arbitrary base flow is recalled and specific applications to acoustics are presented. The implementation of the noise source detection method for two-dimensional weakly compressible (low Mach number) flows is discussed, and the applicability of the method is demonstrated.
Explicit finite-difference lattice Boltzmann method for curvilinear coordinates.
Guo, Zhaoli; Zhao, T S
2003-06-01
In this paper a finite-difference-based lattice Boltzmann method for curvilinear coordinates is proposed in order to improve the computational efficiency and numerical stability of a recent method [R. Mei and W. Shyy, J. Comput. Phys. 143, 426 (1998)] in which the collision term of the Boltzmann Bhatnagar-Gross-Krook equation for discrete velocities is treated implicitly. In the present method, the implicitness of the numerical scheme is removed by introducing a distribution function different from that being used currently. As a result, an explicit finite-difference lattice Boltzmann method for curvilinear coordinates is obtained. The scheme is applied to a two-dimensional Poiseuille flow, an unsteady Couette flow, a lid-driven cavity flow, and a steady flow around a circular cylinder. The numerical results are in good agreement with the results of previous studies. Extensions to other lattice Boltzmann models based on nonuniform meshes are also discussed.
Lattice Boltzmann method fundamentals and engineering applications with computer codes
Mohamad, A A
2014-01-01
Introducing the Lattice Boltzmann Method in a readable manner, this book provides detailed examples with complete computer codes. It avoids the most complicated mathematics and physics without scarifying the basic fundamentals of the method.
Analysis of spectral methods for the homogeneous Boltzmann equation
Filbet, Francis
2011-04-01
The development of accurate and fast algorithms for the Boltzmann collision integral and their analysis represent a challenging problem in scientific computing and numerical analysis. Recently, several works were devoted to the derivation of spectrally accurate schemes for the Boltzmann equation, but very few of them were concerned with the stability analysis of the method. In particular there was no result of stability except when the method was modified in order to enforce the positivity preservation, which destroys the spectral accuracy. In this paper we propose a new method to study the stability of homogeneous Boltzmann equations perturbed by smoothed balanced operators which do not preserve positivity of the distribution. This method takes advantage of the "spreading" property of the collision, together with estimates on regularity and entropy production. As an application we prove stability and convergence of spectral methods for the Boltzmann equation, when the discretization parameter is large enough (with explicit bound). © 2010 American Mathematical Society.
Lattice Boltzmann modeling of directional wetting: Comparing simulations to experiments
Jansen, H.P.; Sotthewes, K.; Swigchem, van J.; Zandvliet, H.J.W.; Kooij, E.S.
2013-01-01
Lattice Boltzmann Modeling (LBM) simulations were performed on the dynamic behavior of liquid droplets on chemically striped patterned surfaces, ultimately with the aim to develop a predictive tool enabling reliable design of future experiments. The simulations accurately mimic experimental results,
Comparison of Boltzmann Equations with Quantum Dynamics for Scalar Fields
Lindner, Manfred; Lindner, Manfred; Muller, Markus Michael
2006-01-01
Boltzmann equations are often used to study the thermal evolution of particle reaction networks. Prominent examples are the computation of the baryon asymmetry of the universe and the evolution of the quark-gluon plasma after relativistic heavy ion collisions. However, Boltzmann equations are only a classical approximation of the quantum thermalization process which is described by the so-called Kadanoff-Baym equations. This raises the question how reliable Boltzmann equations are as approximations to the full Kadanoff-Baym equations. Therefore, we present in this paper a detailed comparison between the Kadanoff-Baym and Boltzmann equations in the framework of a scalar Phi^4 quantum field theory in 3+1 space-time dimensions. The obtained numerical solutions reveal significant discrepancies in the results predicted by both types of equations. Most notably, apart from quantitative discrepancies, on a qualitative level the universality observed for the Kadanoff-Baym equations is severely restricted in the case o...
Permit Allocation in Emissions Trading using the Boltzmann Distribution
Park, Ji-Won; Isard, Walter
2011-01-01
In emissions trading, the initial permit allocation is an intractable issue because it needs to be essentially fair to the participating countries. There are many ways to distribute a given total amount of emissions permits among countries, but the existing distribution methods such as auctioning and grandfathering have been debated. Here we describe a new model for permit allocation in emissions trading using the Boltzmann distribution. The Boltzmann distribution is introduced to permit allocation by combining it with concepts in emissions trading. A price determination mechanism for emission permits is then developed in relation to the {\\beta} value in the Boltzmann distribution. Finally, it is demonstrated how emissions permits can be practically allocated among participating countries in empirical results. The new allocation model using the Boltzmann distribution describes a most probable, natural, and unbiased distribution of emissions permits among multiple countries. Based on its simplicity and versati...
Computational Aeroacoustics Using the Generalized Lattice Boltzmann Equation Project
National Aeronautics and Space Administration — The overall objective of the proposed project is to develop a generalized lattice Boltzmann (GLB) approach as a potential computational aeroacoustics (CAA) tool for...
High-order regularization in lattice-Boltzmann equations
Mattila, Keijo K.; Philippi, Paulo C.; Hegele, Luiz A.
2017-04-01
A lattice-Boltzmann equation (LBE) is the discrete counterpart of a continuous kinetic model. It can be derived using a Hermite polynomial expansion for the velocity distribution function. Since LBEs are characterized by discrete, finite representations of the microscopic velocity space, the expansion must be truncated and the appropriate order of truncation depends on the hydrodynamic problem under investigation. Here we consider a particular truncation where the non-equilibrium distribution is expanded on a par with the equilibrium distribution, except that the diffusive parts of high-order non-equilibrium moments are filtered, i.e., only the corresponding advective parts are retained after a given rank. The decomposition of moments into diffusive and advective parts is based directly on analytical relations between Hermite polynomial tensors. The resulting, refined regularization procedure leads to recurrence relations where high-order non-equilibrium moments are expressed in terms of low-order ones. The procedure is appealing in the sense that stability can be enhanced without local variation of transport parameters, like viscosity, or without tuning the simulation parameters based on embedded optimization steps. The improved stability properties are here demonstrated using the perturbed double periodic shear layer flow and the Sod shock tube problem as benchmark cases.
Harrod, Steven; Kelton, W. David
2006-01-01
Nonstationary Poisson processes are appropriate in many applications, including disease studies, transportation, finance, and social policy. The authors review the risks of ignoring nonstationarity in Poisson processes and demonstrate three algorithms for generation of Poisson processes with piec......Nonstationary Poisson processes are appropriate in many applications, including disease studies, transportation, finance, and social policy. The authors review the risks of ignoring nonstationarity in Poisson processes and demonstrate three algorithms for generation of Poisson processes...
Maxwell iteration for the lattice Boltzmann method with diffusive scaling.
Zhao, Weifeng; Yong, Wen-An
2017-03-01
In this work, we present an alternative derivation of the Navier-Stokes equations from Bhatnagar-Gross-Krook models of the lattice Boltzmann method with diffusive scaling. This derivation is based on the Maxwell iteration and can expose certain important features of the lattice Boltzmann solutions. Moreover, it will be seen to be much more straightforward and logically clearer than the existing approaches including the Chapman-Enskog expansion.
Upper Maxwellian bounds for the spatially homogeneous Boltzmann equation
Gamba, I. M.; Panferov, V.; Villani, C.
2007-01-01
For the spatially homogeneous Boltzmann equation with cutoff hard potentials it is shown that solutions remain bounded from above, uniformly in time, by a Maxwellian distribution, provided the initial data have a Maxwellian upper bound. The main technique is based on a comparison principle that uses a certain dissipative property of the linear Boltzmann equation. Implications of the technique to propagation of upper Maxwellian bounds in the spatially-inhomogeneous case are discussed.
A new lattice Boltzmann model for incompressible magnetohydrodynamics
Chen Xing-Wang; Shi Bao-Chang
2005-01-01
Most of the existing lattice Boltzmann magnetohydrodynamics (MHD) models can be viewed as compressible schemes to simulate incompressible MHD flows. The compressible effect might lead to some undesired errors in numerical simulations. In this paper a new incompressible lattice Boltzmann MHD model without compressible effect is presented for simulating incompressible MHD flows. Numerical simulations of the Hartmann flow are performed. We do numerous tests and make comparison with Dellar's model in detail. The numerical results are in good agreement with the analytical error.
[Welding arc temperature field measurements based on Boltzmann spectrometry].
Si, Hong; Hua, Xue-Ming; Zhang, Wang; Li, Fang; Xiao, Xiao
2012-09-01
Arc plasma, as non-uniform plasma, has complicated energy and mass transport processes in its internal, so plasma temperature measurement is of great significance. Compared with absolute spectral line intensity method and standard temperature method, Boltzmann plot measuring is more accurate and convenient. Based on the Boltzmann theory, the present paper calculates the temperature distribution of the plasma and analyzes the principle of lines selection by real time scanning the space of the TIG are measurements.
Boltzmann Samplers for v-balanced Colored Necklaces
Bodini, Olivier
2009-01-01
This paper is devoted to the random generation of particular colored necklaces for which the number of beads of a given color is constrained (these necklaces are called v-balanced). We propose an efficient sampler (its expected time complexity is linear) which satisfies the Boltzmann model principle introduced by Duchon, Flajolet, Louchard and Schaeffer. Our main motivation is to show that the absence of a decomposable specification can be circumvented by mixing the Boltzmann samplers with other types of samplers.
Application of wavelets to a Poisson equation solver and its parallel processing
Tanaka, Nobuatsu [Toshiba Corp., Kawasaki, Kanagawa (Japan)
1998-03-01
This paper describes a powerful and simple new wavelet-based preconditioning method for the CG solvers of Poisson equation. The equation can be solved with an iterative matrix solver, however, in the absence of our method, the computing time will increase exponentially with respect to an increase in grid points. Use of our technique leads to a matrix with a bounded condition number so that computing time is reduced significantly. Results from our numerical experiments confirm the power and accuracy of our wavelet-based preconditioning method. Unlike many preconditioning methods which are not suitable for vector and parallel processing, our algorithm can take advantage of the extra processing capabilities and enhance computing performance. For example, a speed up of over 100 fold can be achieved when solving Poisson equations on a Cray T3D using 128 processors in parallel. (author)
Meshless lattice Boltzmann method for the simulation of fluid flows.
Musavi, S Hossein; Ashrafizaadeh, Mahmud
2015-02-01
A meshless lattice Boltzmann numerical method is proposed. The collision and streaming operators of the lattice Boltzmann equation are separated, as in the usual lattice Boltzmann models. While the purely local collision equation remains the same, we rewrite the streaming equation as a pure advection equation and discretize the resulting partial differential equation using the Lax-Wendroff scheme in time and the meshless local Petrov-Galerkin scheme based on augmented radial basis functions in space. The meshless feature of the proposed method makes it a more powerful lattice Boltzmann solver, especially for cases in which using meshes introduces significant numerical errors into the solution, or when improving the mesh quality is a complex and time-consuming process. Three well-known benchmark fluid flow problems, namely the plane Couette flow, the circular Couette flow, and the impulsively started cylinder flow, are simulated for the validation of the proposed method. Excellent agreement with analytical solutions or with previous experimental and numerical results in the literature is observed in all the simulations. Although the computational resources required for the meshless method per node are higher compared to that of the standard lattice Boltzmann method, it is shown that for cases in which the total number of nodes is significantly reduced, the present method actually outperforms the standard lattice Boltzmann method.
Contravariant Gravity on Poisson Manifolds and Einstein Gravity
Kaneko, Yukio; Watamura, Satoshi
2016-01-01
A relation between a gravity on Poisson manifolds proposed in arXiv:1508.05706 and the Einstein gravity is investigated. The compatibility of the Poisson and Riemann structures defines a unique connection, the contravariant Levi-Civita connection, and leads to the idea of the contravariant gravity. The Einstein-Hilbert-type action includes couplings between the metric and the Poisson tensor. The Weyl transformation is studied to reveal properties of those interactions. It is argued that the theory can have an equivalent description in terms of the Einstein gravity coupled to matter. As an example, it is shown that the contravariant gravity on a two-dimensional Poisson manifold has another description by a real scalar field coupling to the metric in a specific manner.
Modified Regression Correlation Coefficient for Poisson Regression Model
Kaengthong, Nattacha; Domthong, Uthumporn
2017-09-01
This study gives attention to indicators in predictive power of the Generalized Linear Model (GLM) which are widely used; however, often having some restrictions. We are interested in regression correlation coefficient for a Poisson regression model. This is a measure of predictive power, and defined by the relationship between the dependent variable (Y) and the expected value of the dependent variable given the independent variables [E(Y|X)] for the Poisson regression model. The dependent variable is distributed as Poisson. The purpose of this research was modifying regression correlation coefficient for Poisson regression model. We also compare the proposed modified regression correlation coefficient with the traditional regression correlation coefficient in the case of two or more independent variables, and having multicollinearity in independent variables. The result shows that the proposed regression correlation coefficient is better than the traditional regression correlation coefficient based on Bias and the Root Mean Square Error (RMSE).
Doubly stochastic Poisson processes in artificial neural learning.
Card, H C
1998-01-01
This paper investigates neuron activation statistics in artificial neural networks employing stochastic arithmetic. It is shown that a doubly stochastic Poisson process is an appropriate model for the signals in these circuits.
Transforming spatial point processes into Poisson processes using random superposition
Møller, Jesper; Berthelsen, Kasper Klitgaaard
with a complementary spatial point process Y to obtain a Poisson process X∪Y with intensity function β. Underlying this is a bivariate spatial birth-death process (Xt,Yt) which converges towards the distribution of (X,Y). We study the joint distribution of X and Y, and their marginal and conditional distributions...... process with intensity function β if and only if the true Papangelou intensity is used. Whether the superposition is actually such a Poisson process can easily be examined using well known results and fast simulation procedures for Poisson processes. We illustrate this approach to model checking....... In particular, we introduce a fast and easy simulation procedure for Y conditional on X. This may be used for model checking: given a model for the Papangelou intensity of the original spatial point process, this model is used to generate the complementary process, and the resulting superposition is a Poisson...
Modeling laser velocimeter signals as triply stochastic Poisson processes
Mayo, W. T., Jr.
1976-01-01
Previous models of laser Doppler velocimeter (LDV) systems have not adequately described dual-scatter signals in a manner useful for analysis and simulation of low-level photon-limited signals. At low photon rates, an LDV signal at the output of a photomultiplier tube is a compound nonhomogeneous filtered Poisson process, whose intensity function is another (slower) Poisson process with the nonstationary rate and frequency parameters controlled by a random flow (slowest) process. In the present paper, generalized Poisson shot noise models are developed for low-level LDV signals. Theoretical results useful in detection error analysis and simulation are presented, along with measurements of burst amplitude statistics. Computer generated simulations illustrate the difference between Gaussian and Poisson models of low-level signals.
Evolution of fermionic systems as an expectation over Poisson processes
Beccaria, M; De Angelis, G F; Lasinio, G J; Beccaria, Matteo; Presilla, Carlo; Angelis, Gian Fabrizio De; Lasinio, Giovanni Jona
1999-01-01
We derive an exact probabilistic representation for the evolution of a Hubbard model with site- and spin-dependent hopping coefficients and site-dependent interactions in terms of an associated stochastic dynamics of a collection of Poisson processes.
Evolution of Fermionic Systems as AN Expectation Over Poisson Processes
Beccaria, M.; Presilla, C.; de Angelis, G. F.; Jona-Lasinio, G.
We derive an exact probabilistic representation for the evolution of a Hubbard model with site- and spin-dependent hopping coefficients and site-dependent interactions in terms of an associated stochastic dynamics of a collection of Poisson processes.
2D Poisson sigma models with gauged vectorial supersymmetry
Bonezzi, Roberto; Sundell, Per; Torres-Gomez, Alexander
2015-08-01
In this note, we gauge the rigid vectorial supersymmetry of the two-dimensional Poisson sigma model presented in arXiv:1503.05625. We show that the consistency of the construction does not impose any further constraints on the differential Poisson algebra geometry than those required for the ungauged model. We conclude by proposing that the gauged model provides a first-quantized framework for higher spin gravity.
Algebraic structure and Poisson method for a weakly nonholonomic system
无
2011-01-01
The algebraic structure and the Poisson method for a weakly nonholonomic system are studied.The differential equations of motion of the system can be written in a contravariant algebra form and its algebraic structure is discussed.The Poisson theory for the systems which possess Lie algebra structure is generalized to the weakly nonholonomic system.An example is given to illustrate the application of the result.
2D Poisson sigma models with gauged vectorial supersymmetry
Bonezzi, Roberto [Dipartimento di Fisica ed Astronomia, Università di Bologna and INFN, Sezione di Bologna,via Irnerio 46, I-40126 Bologna (Italy); Departamento de Ciencias Físicas, Universidad Andres Bello,Republica 220, Santiago (Chile); Sundell, Per [Departamento de Ciencias Físicas, Universidad Andres Bello,Republica 220, Santiago (Chile); Torres-Gomez, Alexander [Departamento de Ciencias Físicas, Universidad Andres Bello,Republica 220, Santiago (Chile); Instituto de Ciencias Físicas y Matemáticas, Universidad Austral de Chile-UACh,Valdivia (Chile)
2015-08-12
In this note, we gauge the rigid vectorial supersymmetry of the two-dimensional Poisson sigma model presented in arXiv:1503.05625. We show that the consistency of the construction does not impose any further constraints on the differential Poisson algebra geometry than those required for the ungauged model. We conclude by proposing that the gauged model provides a first-quantized framework for higher spin gravity.
Spatial Brownian motion in renormalized Poisson potential: A critical case
Chen, Xia
2011-01-01
Let $B_s$ be a three dimensional Brownian motion and $\\omega(dx)$ be an independent Poisson field on $\\mathbb{R}^3$. It is proved that for any $t>0$, conditionally on $\\omega(\\cdot)$, \\label{*} \\mathbb{E}_0 \\exp\\{\\theta \\int_0^t \\bar{V}(B_s) ds\\} \\ 1/16, where $\\bar{V}(x)$ is the renormalized Poisson potential
2D Poisson sigma models with gauged vectorial supersymmetry
2015-01-01
In this note, we gauge the rigid vectorial supersymmetry of the two-dimensional Poisson sigma model presented in arXiv:1503.05625. We show that the consistency of the construction does not impose any further constraints on the differential Poisson algebra geometry than those required for the ungauged model. We conclude by proposing that the gauged model provides a first-quantized framework for higher spin gravity.
2D Poisson Sigma Models with Gauged Vectorial Supersymmetry
Bonezzi, Roberto; Torres-Gomez, Alexander
2015-01-01
In this note, we gauge the rigid vectorial supersymmetry of the two-dimensional Poisson sigma model presented in arXiv:1503.05625. We show that the consistency of the construction does not impose any further constraints on the differential Poisson algebra geometry than those required for the ungauged model. We conclude by proposing that the gauged model provides a first-quantized framework for higher spin gravity.
On the One Dimensional Poisson Random Geometric Graph
L. Decreusefond
2011-01-01
Full Text Available Given a Poisson process on a bounded interval, its random geometric graph is the graph whose vertices are the points of the Poisson process, and edges exist between two points if and only if their distance is less than a fixed given threshold. We compute explicitly the distribution of the number of connected components of this graph. The proof relies on inverting some Laplace transforms.
Accurate lineshape spectroscopy and the Boltzmann constant.
Truong, G-W; Anstie, J D; May, E F; Stace, T M; Luiten, A N
2015-10-14
Spectroscopy has an illustrious history delivering serendipitous discoveries and providing a stringent testbed for new physical predictions, including applications from trace materials detection, to understanding the atmospheres of stars and planets, and even constraining cosmological models. Reaching fundamental-noise limits permits optimal extraction of spectroscopic information from an absorption measurement. Here, we demonstrate a quantum-limited spectrometer that delivers high-precision measurements of the absorption lineshape. These measurements yield a very accurate measurement of the excited-state (6P1/2) hyperfine splitting in Cs, and reveals a breakdown in the well-known Voigt spectral profile. We develop a theoretical model that accounts for this breakdown, explaining the observations to within the shot-noise limit. Our model enables us to infer the thermal velocity dispersion of the Cs vapour with an uncertainty of 35 p.p.m. within an hour. This allows us to determine a value for Boltzmann's constant with a precision of 6 p.p.m., and an uncertainty of 71 p.p.m.
Extended lattice Boltzmann scheme for droplet combustion
Ashna, Mostafa; Rahimian, Mohammad Hassan; Fakhari, Abbas
2017-05-01
The available lattice Boltzmann (LB) models for combustion or phase change are focused on either single-phase flow combustion or two-phase flow with evaporation assuming a constant density for both liquid and gas phases. To pave the way towards simulation of spray combustion, we propose a two-phase LB method for modeling combustion of liquid fuel droplets. We develop an LB scheme to model phase change and combustion by taking into account the density variation in the gas phase and accounting for the chemical reaction based on the Cahn-Hilliard free-energy approach. Evaporation of liquid fuel is modeled by adding a source term, which is due to the divergence of the velocity field being nontrivial, in the continuity equation. The low-Mach-number approximation in the governing Navier-Stokes and energy equations is used to incorporate source terms due to heat release from chemical reactions, density variation, and nonluminous radiative heat loss. Additionally, the conservation equation for chemical species is formulated by including a source term due to chemical reaction. To validate the model, we consider the combustion of n-heptane and n -butanol droplets in stagnant air using overall single-step reactions. The diameter history and flame standoff ratio obtained from the proposed LB method are found to be in good agreement with available numerical and experimental data. The present LB scheme is believed to be a promising approach for modeling spray combustion.
Lattice Boltzmann model for resistive relativistic magnetohydrodynamics.
Mohseni, F; Mendoza, M; Succi, S; Herrmann, H J
2015-08-01
In this paper, we develop a lattice Boltzmann model for relativistic magnetohydrodynamics (MHD). Even though the model is derived for resistive MHD, it is shown that it is numerically robust even in the high conductivity (ideal MHD) limit. In order to validate the numerical method, test simulations are carried out for both ideal and resistive limits, namely the propagation of Alfvén waves in the ideal MHD and the evolution of current sheets in the resistive regime, where very good agreement is observed comparing to the analytical results. Additionally, two-dimensional magnetic reconnection driven by Kelvin-Helmholtz instability is studied and the effects of different parameters on the reconnection rate are investigated. It is shown that the density ratio has a negligible effect on the magnetic reconnection rate, while an increase in shear velocity decreases the reconnection rate. Additionally, it is found that the reconnection rate is proportional to σ-1/2, σ being the conductivity, which is in agreement with the scaling law of the Sweet-Parker model. Finally, the numerical model is used to study the magnetic reconnection in a stellar flare. Three-dimensional simulation suggests that the reconnection between the background and flux rope magnetic lines in a stellar flare can take place as a result of a shear velocity in the photosphere.
Extended lattice Boltzmann scheme for droplet combustion.
Ashna, Mostafa; Rahimian, Mohammad Hassan; Fakhari, Abbas
2017-05-01
The available lattice Boltzmann (LB) models for combustion or phase change are focused on either single-phase flow combustion or two-phase flow with evaporation assuming a constant density for both liquid and gas phases. To pave the way towards simulation of spray combustion, we propose a two-phase LB method for modeling combustion of liquid fuel droplets. We develop an LB scheme to model phase change and combustion by taking into account the density variation in the gas phase and accounting for the chemical reaction based on the Cahn-Hilliard free-energy approach. Evaporation of liquid fuel is modeled by adding a source term, which is due to the divergence of the velocity field being nontrivial, in the continuity equation. The low-Mach-number approximation in the governing Navier-Stokes and energy equations is used to incorporate source terms due to heat release from chemical reactions, density variation, and nonluminous radiative heat loss. Additionally, the conservation equation for chemical species is formulated by including a source term due to chemical reaction. To validate the model, we consider the combustion of n-heptane and n-butanol droplets in stagnant air using overall single-step reactions. The diameter history and flame standoff ratio obtained from the proposed LB method are found to be in good agreement with available numerical and experimental data. The present LB scheme is believed to be a promising approach for modeling spray combustion.
A lattice Boltzmann study of non-hydrodynamic effects in shell models of turbulence
Benzi, R.; Biferale, L.; Sbragaglia, M.; Succi, S.; Toschi, F.
2004-10-01
A lattice Boltzmann scheme simulating the dynamics of shell models of turbulence is developed. The influence of high-order kinetic modes (ghosts) on the dissipative properties of turbulence dynamics is studied. It is analytically found that when ghost fields relax on the same timescale as the hydrodynamic ones, their major effect is a net enhancement of the fluid viscosity. The bare fluid viscosity is recovered by letting ghost fields evolve on a much longer timescale. Analytical results are borne out by high-resolution numerical simulations. These simulations indicate that the hydrodynamic manifold is very robust towards large fluctuations of non-hydrodynamic fields.
Lattice Boltzmann simulations for proton transport in 2-D model channels of Nafion.
Akinaga, Yoshinobu; Hyodo, Shi-aki; Ikeshoji, Tamio
2008-10-01
Proton conductance in a 2-D channel with a slab-like structure was studied to verify that the lattice Boltzmann method (LBM) can be used as a simulation tool for proton conduction in a Nafion membrane, which is a mesoscopic system with a highly disordered porous structure. Diffusion resulting from a concentration gradient and migration by an electrostatic force were considered as the origins of proton transport. The electrostatic force acting on a proton was computed by solving the Poisson equation. The proton concentration in the membrane is expressed as a continuous function and the sulfonic charge is placed discretely. The space-averaged conductance of protons in a nonequilibrium stationary state was evaluated as a function of the structural parameters: namely, channel width and distribution of the sulfonic groups. The resulting space-averaged conductance deviates from the bulk values, depending particularly on the sulfonic group distribution. Details of the simulation scheme are described and the applicability of the present scheme to real membranes is discussed.
Lattice Boltzmann method and its applications in engineering thermophysics
HE YaLing; LI Qing; WANG Yong; TANG GuiHua
2009-01-01
The lattice Boltzmann method (LBM),a mesoscopic method between the molecular dynamics method and the conventional numerical methods,has been developed into a very efficient numerical alternative in the past two decades.Unlike conventional numerical methods,the kinetic theory based LBM simulates fluid flows by tracking the evolution of the particle distribution function,and then accumulates the distribution to obtain macroscopic averaged properties.In this article we review some work on LBM applications in engineering thermophysics:(1) brief introduction to the development of the LBM; (2)fundamental theory of LBM including the Boltzmann equation,Maxwell distribution function,Boltzmann-BGK equation,and the lattice Boltzmann-BGK equation; (3) lattice Boltzmann models for compressible flows and non-equilibrium gas flows,bounce back-specular-reflection boundary scheme for microscale gaseous flows,the mass modified outlet boundary scheme for fully developed flows,and an implicit-explicit finite-difference-based LBM; and (4) applications of the LBM to oscillating flow,compressible flow,porous media flow,non-equilibrium flow,and gas resonant oscillating flow.
Completely Integrable Hamiltonian Systems Generated by Poisson Structures in R3
LEI De-Chao; ZHANG Xiang
2005-01-01
@@ The completely integrable Hamiltonian systems have been applied to physics and mechanics intensively. We generate a family of completely integrable Hamiltonian systems from some kinds of exact Poisson structures in R3 by the realization of the Poisson algebra. Moreover, we prove that there is a Poisson algebra which cannot be realized by an exact Poisson structure.
Semiclassical Limits of Ore Extensions and a Poisson Generalized Weyl Algebra
Cho, Eun-Hee; Oh, Sei-Qwon
2016-07-01
We observe [Launois and Lecoutre, Trans. Am. Math. Soc. 368:755-785, 2016, Proposition 4.1] that Poisson polynomial extensions appear as semiclassical limits of a class of Ore extensions. As an application, a Poisson generalized Weyl algebra A 1, considered as a Poisson version of the quantum generalized Weyl algebra, is constructed and its Poisson structures are studied. In particular, a necessary and sufficient condition is obtained, such that A 1 is Poisson simple and established that the Poisson endomorphisms of A 1 are Poisson analogues of the endomorphisms of the quantum generalized Weyl algebra.
Lattice Boltzmann Model for Compressible Fluid on a Square Lattice
SUN Cheng-Hai
2000-01-01
A two-level four-direction lattice Boltzmann model is formulated on a square lattice to simulate compressible flows with a high Mach number. The particle velocities are adaptive to the mean velocity and internal energy. Therefore, the mean flow can have a high Mach number. Due to the simple form of the equilibrium distribution, the 4th order velocity tensors are not involved in the calculations. Unlike the standard lattice Boltzmann model, o special treatment is need for the homogeneity of 4th order velocity tensors on square lattices. The Navier-Stokes equations were derived by the Chapman-Enskog method from the BGK Boltzmann equation. The model can be easily extended to three-dimensional cubic lattices. Two-dimensional shock-wave propagation was simulated
Navier-Stokes Dynamics by a Discrete Boltzmann Model
Rubinstein, Robet
2010-01-01
This work investigates the possibility of particle-based algorithms for the Navier-Stokes equations and higher order continuum approximations of the Boltzmann equation; such algorithms would generalize the well-known Pullin scheme for the Euler equations. One such method is proposed in the context of a discrete velocity model of the Boltzmann equation. Preliminary results on shock structure are consistent with the expectation that the shock should be much broader than the near discontinuity predicted by the Pullin scheme, yet narrower than the prediction of the Boltzmann equation. We discuss the extension of this essentially deterministic method to a stochastic particle method that, like DSMC, samples the distribution function rather than resolving it completely.
Caveat on the Boltzmann distribution function use in biology.
Sevcik, Carlos
2017-08-01
Sigmoid semilogarithmic functions with shape of Boltzmann equations, have become extremely popular to describe diverse biological situations. Part of the popularity is due to the easy availability of software which fits Boltzmann functions to data, without much knowledge of the fitting procedure or the statistical properties of the parameters derived from the procedure. The purpose of this paper is to explore the plasticity of the Boltzmann function to fit data, some aspects of the optimization procedure to fit the function to data and how to use this plastic function to differentiate the effect of treatment on data and to attest the statistical significance of treatment effect on the data. Copyright © 2017. Published by Elsevier Ltd.
Physical scales in the Wigner-Boltzmann equation.
Nedjalkov, M; Selberherr, S; Ferry, D K; Vasileska, D; Dollfus, P; Querlioz, D; Dimov, I; Schwaha, P
2013-01-01
The Wigner-Boltzmann equation provides the Wigner single particle theory with interactions with bosonic degrees of freedom associated with harmonic oscillators, such as phonons in solids. Quantum evolution is an interplay of two transport modes, corresponding to the common coherent particle-potential processes, or to the decoherence causing scattering due to the oscillators. Which evolution mode will dominate depends on the scales of the involved physical quantities. A dimensionless formulation of the Wigner-Boltzmann equation is obtained, where these scales appear as dimensionless strength parameters. A notion called scaling theorem is derived, linking the strength parameters to the coupling with the oscillators. It is shown that an increase of this coupling is equivalent to a reduction of both the strength of the electric potential, and the coherence length. Secondly, the existence of classes of physically different, but mathematically equivalent setups of the Wigner-Boltzmann evolution is demonstrated.
Lattice Boltzmann Large Eddy Simulation Model of MHD
Flint, Christopher
2016-01-01
The work of Ansumali \\textit{et al.}\\cite{Ansumali} is extended to Two Dimensional Magnetohydrodynamic (MHD) turbulence in which energy is cascaded to small spatial scales and thus requires subgrid modeling. Applying large eddy simulation (LES) modeling of the macroscopic fluid equations results in the need to apply ad-hoc closure schemes. LES is applied to a suitable mesoscopic lattice Boltzmann representation from which one can recover the MHD equations in the long wavelength, long time scale Chapman-Enskog limit (i.e., the Knudsen limit). Thus on first performing filter width expansions on the lattice Boltzmann equations followed by the standard small Knudsen expansion on the filtered lattice Boltzmann system results in a closed set of MHD turbulence equations provided we enforce the physical constraint that the subgrid effects first enter the dynamics at the transport time scales. In particular, a multi-time relaxation collision operator is considered for the density distribution function and a single rel...
An integrable 3D lattice model with positive Boltzmann weights
Mangazeev, Vladimir V; Sergeev, Sergey M
2013-01-01
In this paper we construct a three-dimensional (3D) solvable lattice model with non-negative Boltzmann weights. The spin variables in the model are assigned to edges of the 3D cubic lattice and run over an infinite number of discrete states. The Boltzmann weights satisfy the tetrahedron equation, which is a 3D generalisation of the Yang-Baxter equation. The weights depend on a free parameter 0Boltzmann weights.
Mutation-Periodic Quivers, Integrable Maps and Associated Poisson Algebras
Fordy, Allan P
2010-01-01
We consider a class of map, recently derived in the context of cluster mutation. In this paper we start with a brief review of the quiver context, but then move onto a discussion of a related Poisson bracket, along with the Poisson algebra of a special family of functions associated with these maps. A bi-Hamiltonian structure is derived and used to construct a sequence of Poisson commuting functions and hence show complete integrability. Canonical coordinates are derived, with the map now being a canonical transformation with a sequence of commuting invariant functions. Compatibility of a pair of these functions gives rise to Liouville's equation and the map plays the role of a B\\"acklund transformation.
The coupling of Poisson sigma models to topological backgrounds
Rosa, Dario
2016-01-01
We extend the coupling to the topological backgrounds, recently worked out for the 2-dimensional BF-model, to the most general Poisson sigma models. The coupling involves the choice of a Casimir function on the target manifold and modifies the BRST transformations. This in turn induces a change in the BRST cohomology of the resulting theory. The observables of the coupled theory are analyzed and their geometrical intrepretation is given. We finally couple the theory to 2-dimensional topological gravity: this is the first step to study a topological string theory in propagation on a Poisson manifold. As an application, we show that the gauge-fixed vectorial supersymmetry of the Poisson sigma models has a natural explanation in terms of the theory coupled to topological gravity.
POISSON LIMIT THEOREM FOR COUNTABLE MARKOV CHAINS IN MARKOVIAN ENVIRONMENTS
方大凡; 王汉兴; 唐矛宁
2003-01-01
A countable Markov chain in a Markovian environment is considered. A Poisson limit theorem for the chain recurring to small cylindrical sets is mainly achieved. In order to prove this theorem, the entropy function h is introduced and the Shannon-McMillan-Breiman theorem for the Markov chain in a Markovian environment is shown. It' s well-known that a Markov process in a Markovian environment is generally not a standard Markov chain, so an example of Poisson approximation for a process which is not a Markov process is given. On the other hand, when the environmental process degenerates to a constant sequence, a Poisson limit theorem for countable Markov chains, which is the generalization of Pitskel's result for finite Markov chains is obtained.
The coupling of Poisson sigma models to topological backgrounds
Rosa, Dario [School of Physics, Korea Institute for Advanced Study,Seoul 02455 (Korea, Republic of)
2016-12-13
We extend the coupling to the topological backgrounds, recently worked out for the 2-dimensional BF-model, to the most general Poisson sigma models. The coupling involves the choice of a Casimir function on the target manifold and modifies the BRST transformations. This in turn induces a change in the BRST cohomology of the resulting theory. The observables of the coupled theory are analyzed and their geometrical interpretation is given. We finally couple the theory to 2-dimensional topological gravity: this is the first step to study a topological string theory in propagation on a Poisson manifold. As an application, we show that the gauge-fixed vectorial supersymmetry of the Poisson sigma models has a natural explanation in terms of the theory coupled to topological gravity.
Segmentation algorithm for non-stationary compound Poisson processes
Toth, Bence; Farmer, J Doyne
2010-01-01
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 the time series. The process is composed of consecutive patches of variable length, each patch being described by a stationary compound Poisson process, i.e. a Poisson process where each count is associated to 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-Galvan, et al., Phys. Rev. Lett., 87, 168105 (2001). We show that the new algorithm outperforms the original one for regime switching 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.
Blocked Shape Memory Effect in Negative Poisson's Ratio Polymer Metamaterials.
Boba, Katarzyna; Bianchi, Matteo; McCombe, Greg; Gatt, Ruben; Griffin, Anselm C; Richardson, Robert M; Scarpa, Fabrizio; Hamerton, Ian; Grima, Joseph N
2016-08-10
We describe a new class of negative Poisson's ratio (NPR) open cell PU-PE foams produced by blocking the shape memory effect in the polymer. Contrary to classical NPR open cell thermoset and thermoplastic foams that return to their auxetic phase after reheating (and therefore limit their use in technological applications), this new class of cellular solids has a permanent negative Poisson's ratio behavior, generated through multiple shape memory (mSM) treatments that lead to a fixity of the topology of the cell foam. The mSM-NPR foams have Poisson's ratio values similar to the auxetic foams prior their return to the conventional phase, but compressive stress-strain curves similar to the ones of conventional foams. The results show that by manipulating the shape memory effect in polymer microstructures it is possible to obtain new classes of materials with unusual deformation mechanisms.
Markov modulated Poisson process models incorporating covariates for rainfall intensity.
Thayakaran, R; Ramesh, N I
2013-01-01
Time series of rainfall bucket tip times at the Beaufort Park station, Bracknell, in the UK are modelled by a class of Markov modulated Poisson processes (MMPP) which may be thought of as a generalization of the Poisson process. Our main focus in this paper is to investigate the effects of including covariate information into the MMPP model framework on statistical properties. In particular, we look at three types of time-varying covariates namely temperature, sea level pressure, and relative humidity that are thought to be affecting the rainfall arrival process. Maximum likelihood estimation is used to obtain the parameter estimates, and likelihood ratio tests are employed in model comparison. Simulated data from the fitted model are used to make statistical inferences about the accumulated rainfall in the discrete time interval. Variability of the daily Poisson arrival rates is studied.
Super-Affine Hierarchies and their Poisson Embeddings
Toppan, F
1998-01-01
The link between (super)-affine Lie algebras as Poisson brackets structures and integrable hierarchies provides both a classification and a tool for obtaining superintegrable hierarchies. The lack of a fully systematic procedure for constructing matrix-type Lax operators, which makes the supersymmetric case essentially different from the bosonic counterpart, is overcome via the notion of Poisson embeddings (P.E.), i.e. Poisson mappings relating affine structures to conformal structures (in their simplest version P.E. coincide with the Sugawara construction). A full class of hierarchies can be recovered by using uniquely Lie-algebraic notions. The group-algebraic properties implicit in the super-affine picture allow a systematic derivation of reduced hierarchies by imposing either coset conditions or hamiltonian constraints (or possibly both).
Poisson Packet Traffic Generation Based on Empirical Data
Andrej Kos
2003-10-01
Full Text Available An algorithm for generating equivalent Poisson packet traffic based on empirical traffic data is presented in this paper. Two steps are required in order to produce equivalent Poisson packet traffic. Real traffic trace is analyzed in the first step. In the second step, a new equivalent synthetic Poisson traffic is generated in such a way that the first order statistical parameters remain unchanged. New packet inter-arrival time series are produced in a random manner using negative exponential probability distribution with a known mean. New packet size series are also produced in a random manner. However, due to specified minimum and maximum packet sizes, a truncated exponential probability distribution is applied.
Effect of Poisson noise on adiabatic quantum control
Kiely, A.; Muga, J. G.; Ruschhaupt, A.
2017-01-01
We present a detailed derivation of the master equation describing a general time-dependent quantum system with classical Poisson white noise and outline its various properties. We discuss the limiting cases of Poisson white noise and provide approximations for the different noise strength regimes. We show that using the eigenstates of the noise superoperator as a basis can be a useful way of expressing the master equation. Using this, we simulate various settings to illustrate different effects of Poisson noise. In particular, we show a dip in the fidelity as a function of noise strength where high fidelity can occur in the strong-noise regime for some cases. We also investigate recent claims [J. Jing et al., Phys. Rev. A 89, 032110 (2014), 10.1103/PhysRevA.89.032110] that this type of noise may improve rather than destroy adiabaticity.
Suppressing Background Radiation Using Poisson Principal Component Analysis
Tandon, P; Dubrawski, A; Labov, S; Nelson, K
2016-01-01
Performance of nuclear threat detection systems based on gamma-ray spectrometry often strongly depends on the ability to identify the part of measured signal that can be attributed to background radiation. We have successfully applied a method based on Principal Component Analysis (PCA) to obtain a compact null-space model of background spectra using PCA projection residuals to derive a source detection score. We have shown the method's utility in a threat detection system using mobile spectrometers in urban scenes (Tandon et al 2012). While it is commonly assumed that measured photon counts follow a Poisson process, standard PCA makes a Gaussian assumption about the data distribution, which may be a poor approximation when photon counts are low. This paper studies whether and in what conditions PCA with a Poisson-based loss function (Poisson PCA) can outperform standard Gaussian PCA in modeling background radiation to enable more sensitive and specific nuclear threat detection.
The coupling of Poisson sigma models to topological backgrounds
Rosa, Dario
2016-12-01
We extend the coupling to the topological backgrounds, recently worked out for the 2-dimensional BF-model, to the most general Poisson sigma models. The coupling involves the choice of a Casimir function on the target manifold and modifies the BRST transformations. This in turn induces a change in the BRST cohomology of the resulting theory. The observables of the coupled theory are analyzed and their geometrical interpretation is given. We finally couple the theory to 2-dimensional topological gravity: this is the first step to study a topological string theory in propagation on a Poisson manifold. As an application, we show that the gauge-fixed vectorial supersymmetry of the Poisson sigma models has a natural explanation in terms of the theory coupled to topological gravity.
On a Boltzmann-type price formation model
Burger, Martin
2013-06-26
In this paper, we present a Boltzmann-type price formation model, which is motivated by a parabolic free boundary model for the evolution of price presented by Lasry and Lions in 2007. We discuss the mathematical analysis of the Boltzmann-type model and show that its solutions converge to solutions of the model by Lasry and Lions as the transaction rate tends to infinity. Furthermore, we analyse the behaviour of the initial layer on the fast time scale and illustrate the price dynamics with various numerical experiments. © 2013 The Author(s) Published by the Royal Society. All rights reserved.
Revisiting Boltzmann learning: parameter estimation in Markov random fields
Hansen, Lars Kai; Andersen, Lars Nonboe; Kjems, Ulrik
1996-01-01
This article presents a generalization of the Boltzmann machine that allows us to use the learning rule for a much wider class of maximum likelihood and maximum a posteriori problems, including both supervised and unsupervised learning. Furthermore, the approach allows us to discuss regularization...... and generalization in the context of Boltzmann machines. We provide an illustrative example concerning parameter estimation in an inhomogeneous Markov field. The regularized adaptation produces a parameter set that closely resembles the “teacher” parameters, hence, will produce segmentations that closely reproduce...
Boundary Conditions for Free Interfaces with the Lattice Boltzmann Method
Bogner, Simon; Rüde, Ulrich
2014-01-01
In this paper we analyze the boundary treatment of the Lattice Boltzmann method for simulating 3D flows with free surfaces. The widely used free surface boundary condition of K\\"orner et al. (2005) is shown to be first order accurate. The article presents new free surface boundary schemes that are suitable for the lattice Boltzmann method and that have second order spatial accuracy. The new method takes the free boundary position and orientation with respect to the computational lattice into account. Numerical experiments confirm the theoretical findings and illustrate the the difference between the old and the new method.
Spinor Boltzmann Equation with Two Momenta at the Fermi Level
王正川
2012-01-01
Based on the formalism of Keldysh's nonequilibrium Green function, we establish a two momenta spinor Boltzmann equation for longitudinal scalar distribution function and transverse vector distribution function. The lon- gitudinal charge currents, transverse spin currents and the continuity equations satisfied by them are then studied, it indicates that both the charge currents and spin currents decay oscillately along with position, which is due to the momenta integral over the Fermi surface. We also compare our charge currents and spin currents with the corresponding results of one momentum spinor Boltzmann equation, the differences are obvious.
The Boltzmann equation near a rotational local Maxwellian
Kim, Chanwoo
2011-01-01
In rotationally symmetric domains, the Boltzmann equation with specular reflection boundary condition has a special type of equilibrium states called the rotational local Maxwellian which, unlike the uniform Maxwellian, has an additional term related to the angular momentum of the gas. In this paper, we consider the initial boundary value problem of the Boltzmann equation near the rotational local Maxwellian. Based on the L2-L1 framework of [12], we establish the global well-posedness and the convergence toward such equilibrium states.
Acoustic limit of the Boltzmann equation: classical solutions
Jang, Juhi; Jiang, Ning
2009-01-01
We study the acoustic limit from the Boltzmann equation in the framework of classical solutions. For a solution $F_\\varepsilon=\\mu +\\varepsilon \\sqrt{\\mu}f_\\varepsilon$ to the rescaled Boltzmann equation in the acoustic time scaling \\partial_t F_\\varepsilon +\\vgrad F_\\varepsilon =\\frac{1}{\\varepsilon} \\Q(F_\\varepsilon,F_\\varepsilon), inside a periodic box $\\mathbb{T}^3$, we establish the global-in-time uniform energy estimates of $f_\\varepsilon$ in $\\varepsilon$ and prove that $f_\\varepsilon$...
Contact line dynamics in binary lattice Boltzmann simulations
Pooley, C M; Yeomans, J M; 10.1103/PhysRevE.78.056709
2008-01-01
We show that, when a single relaxation time lattice Boltzmann algorithm is used to solve the hydrodynamic equations of a binary fluid for which the two components have different viscosities, strong spurious velocities in the steady state lead to incorrect results for the equilibrium contact angle. We identify the origins of these spurious currents, and demonstrate how the results can be greatly improved by using a lattice Boltzmann method based on a multiple-relaxation-time algorithm. By considering capillary filling we describe the dependence of the advancing contact angle on the interface velocity.
Axisymmetric multiphase Lattice Boltzmann method for generic equations of state
Reijers, Sten A; Toschi, Federico
2015-01-01
We present an axisymmetric lattice Boltzmann model based on the Kupershtokh et al. multiphase model that is capable of solving liquid-gas density ratios up to $10^3$. Appropriate source terms are added to the lattice Boltzmann evolution equation to fully recover the axisymmetric multiphase conservation equations. We validate the model by showing that a stationary droplet obeys the Young-Laplace law, comparing the second oscillation mode of a droplet with respect to an analytical solution and showing correct mass conservation of a propagating density wave.
Two-dimensional lattice Boltzmann model for magnetohydrodynamics.
Schaffenberger, Werner; Hanslmeier, Arnold
2002-10-01
We present a lattice Boltzmann model for the simulation of two-dimensional magnetohydro dynamic (MHD) flows. The model is an extension of a hydrodynamic lattice Boltzman model with 9 velocities on a square lattice resulting in a model with 17 velocities. Earlier lattice Boltzmann models for two-dimensional MHD used a bidirectional streaming rule. However, the use of such a bidirectional streaming rule is not necessary. In our model, the standard streaming rule is used, allowing smaller viscosities. To control the viscosity and the resistivity independently, a matrix collision operator is used. The model is then applied to the Hartmann flow, giving reasonable results.
CORRECTIONS TO THE COLLISION TERM IN THE BGK BOLTZMANN EQUATION
FENG SHI-DE; REN RONG-CAI; CUI XIAO-PENG; JI ZHONG-ZHEN
2001-01-01
With the discrete method of the hexagonal cell and three different velocities of particle population in each cell,a two-dimensional lattice Boltzmann model is developed in this paper.[1,2] The collision operator in the Boltzmann equation is expanded to fourth order using the Taylor expansion.[3,4] With this model, good results have been obtained from the numerical simulation of the reflection phenomenon of the shock wave on the surface of an obstacle, and the numerical stability is also good. Thus the applicability of the D2Q19 model is verified.
Efficient triangulation of Poisson-disk sampled point sets
Guo, Jianwei
2014-05-06
In this paper, we present a simple yet efficient algorithm for triangulating a 2D input domain containing a Poisson-disk sampled point set. The proposed algorithm combines a regular grid and a discrete clustering approach to speedup the triangulation. Moreover, our triangulation algorithm is flexible and performs well on more general point sets such as adaptive, non-maximal Poisson-disk sets. The experimental results demonstrate that our algorithm is robust for a wide range of input domains and achieves significant performance improvement compared to the current state-of-the-art approaches. © 2014 Springer-Verlag Berlin Heidelberg.
Poisson-Fermi Model of Single Ion Activities
Liu, Jinn-Liang
2015-01-01
A Poisson-Fermi model is proposed for calculating activity coefficients of single ions in strong electrolyte solutions based on the experimental Born radii and hydration shells of ions in aqueous solutions. The steric effect of water molecules and interstitial voids in the first and second hydration shells play an important role in our model. The screening and polarization effects of water are also included in the model that can thus describe spatial variations of dielectric permittivity, water density, void volume, and ionic concentration. The activity coefficients obtained by the Poisson-Fermi model with only one adjustable parameter are shown to agree with experimental data, which vary nonmonotonically with salt concentrations.
Adaptive maximal poisson-disk sampling on surfaces
Yan, Dongming
2012-01-01
In this paper, we study the generation of maximal Poisson-disk sets with varying radii on surfaces. Based on the concepts of power diagram and regular triangulation, we present a geometric analysis of gaps in such disk sets on surfaces, which is the key ingredient of the adaptive maximal Poisson-disk sampling framework. Moreover, we adapt the presented sampling framework for remeshing applications. Several novel and efficient operators are developed for improving the sampling/meshing quality over the state-of-theart. © 2012 ACM.
The energy-momentum of a Poisson structure
Buric, M. [University of Belgrade, Faculty of Physics, P.O. Box 368, Belgrade (RS); Madore, J. [Universite de Paris-Sud, Laboratoire de Physique Theorique, Orsay (France); Zoupanos, G. [National Technical University, Physics Department, Zografou, Athens (Greece)
2008-06-15
Consider the quasi-commutative approximation to a noncommutative geometry. It is shown that there is a natural map from the resulting Poisson structure to the Riemann curvature of a metric. This map is applied to the study of high-frequency gravitational radiation. In classical gravity in the WKB approximation there are two results of interest, a dispersion relation and a conservation law. Both of these results can be extended to the noncommutative case, with the difference that they result from a cocycle condition on the high-frequency contribution to the Poisson structure, not from the field equations. (orig.)
Improvement on MLE of the Means of Independent Poisson Distribution
李排昌
2000-01-01
In this paper, we consider the simultaneous estimation of the parameters (means) of the independent Poisson distribution by using the following loss functions: L0(θ，T)=∑i=1n(Ti-θi)2，L1(θ，T)=∑i=1n(Ti-θi)2/θi We develop an estimator which is better than the maximum likelihood estimator X simultaneously under L0(θ, T) and L1(θ, T). Our estimator possesses substantially smaller risk than the usual estimator X to estimate the parameters (means) of the independent Poisson distribution.
Poisson Brackets of Normal-Ordered Wilson Loops
Lee, C. -W. H.; Rajeev, S. G.
1998-01-01
We formulate Yang-Mills theory in terms of the large-N limit, viewed as a classical limit, of gauge-invariant dynamical variables, which are closely related to Wilson loops, via deformation quantization. We obtain a Poisson algebra of these dynamical variables corresponding to normal-ordered quantum (at a finite value of $\\hbar$) operators. Comparing with a Poisson algebra one of us introduced in the past for Weyl-ordered quantum operators, we find, using ideas closly related to topological g...
A high order solver for the unbounded Poisson equation
Hejlesen, Mads Mølholm; Rasmussen, Johannes Tophøj; Chatelain, Philippe
and the integration kernel. In this work we show an implementation of high order regularised integration kernels in the HE algorithm for the unbounded Poisson equation to formally achieve an arbitrary high order convergence. We further present a quantitative study of the convergence rate to give further insight......In mesh-free particle methods a high order solution to the unbounded Poisson equation is usually achieved by constructing regularised integration kernels for the Biot-Savart law. Here the singular, point particles are regularised using smoothed particles to obtain an accurate solution with an order...
? filtering for stochastic systems driven by Poisson processes
Song, Bo; Wu, Zheng-Guang; Park, Ju H.; Shi, Guodong; Zhang, Ya
2015-01-01
This paper investigates the ? filtering problem for stochastic systems driven by Poisson processes. By utilising the martingale theory such as the predictable projection operator and the dual predictable projection operator, this paper transforms the expectation of stochastic integral with respect to the Poisson process into the expectation of Lebesgue integral. Then, based on this, this paper designs an ? filter such that the filtering error system is mean-square asymptotically stable and satisfies a prescribed ? performance level. Finally, a simulation example is given to illustrate the effectiveness of the proposed filtering scheme.
Robust iterative observer for source localization for Poisson equation
Majeed, Muhammad Usman
2017-01-05
Source localization problem for Poisson equation with available noisy boundary data is well known to be highly sensitive to noise. The problem is ill posed and lacks to fulfill Hadamards stability criteria for well posedness. In this work, first a robust iterative observer is presented for boundary estimation problem for Laplace equation, and then this algorithm along with the available noisy boundary data from the Poisson problem is used to localize point sources inside a rectangular domain. The algorithm is inspired from Kalman filter design, however one of the space variables is used as time-like. Numerical implementation along with simulation results is detailed towards the end.
Conditioned Poisson distributions and the concentration of chromatic numbers
Hartigan, John; Tatikonda, Sekhar
2011-01-01
The paper provides a simpler method for proving a delicate inequality that was used by Achlioptis and Naor to establish asymptotic concentration for chromatic numbers of Erdos-Renyi random graphs. The simplifications come from two new ideas. The first involves a sharpened form of a piece of statistical folklore regarding goodness-of-fit tests for two-way tables of Poisson counts under linear conditioning constraints. The second idea takes the form of a new inequality that controls the extreme tails of the distribution of a quadratic form in independent Poissons random variables.
Efficient maximal Poisson-disk sampling and remeshing on surfaces
Guo, Jianwei
2015-02-01
Poisson-disk sampling is one of the fundamental research problems in computer graphics that has many applications. In this paper, we study the problem of maximal Poisson-disk sampling on mesh surfaces. We present a simple approach that generalizes the 2D maximal sampling framework to surfaces. The key observation is to use a subdivided mesh as the sampling domain for conflict checking and void detection. Our approach improves the state-of-the-art approach in efficiency, quality and the memory consumption.
Poisson-Nernst-Planck-Fermi theory for modeling biological ion channels.
Liu, Jinn-Liang; Eisenberg, Bob
2014-12-14
A Poisson-Nernst-Planck-Fermi (PNPF) theory is developed for studying ionic transport through biological ion channels. Our goal is to deal with the finite size of particle using a Fermi like distribution without calculating the forces between the particles, because they are both expensive and tricky to compute. We include the steric effect of ions and water molecules with nonuniform sizes and interstitial voids, the correlation effect of crowded ions with different valences, and the screening effect of water molecules in an inhomogeneous aqueous electrolyte. Including the finite volume of water and the voids between particles is an important new part of the theory presented here. Fermi like distributions of all particle species are derived from the volume exclusion of classical particles. Volume exclusion and the resulting saturation phenomena are especially important to describe the binding and permeation mechanisms of ions in a narrow channel pore. The Gibbs free energy of the Fermi distribution reduces to that of a Boltzmann distribution when these effects are not considered. The classical Gibbs entropy is extended to a new entropy form - called Gibbs-Fermi entropy - that describes mixing configurations of all finite size particles and voids in a thermodynamic system where microstates do not have equal probabilities. The PNPF model describes the dynamic flow of ions, water molecules, as well as voids with electric fields and protein charges. The model also provides a quantitative mean-field description of the charge/space competition mechanism of particles within the highly charged and crowded channel pore. The PNPF results are in good accord with experimental currents recorded in a 10(8)-fold range of Ca(2+) concentrations. The results illustrate the anomalous mole fraction effect, a signature of L-type calcium channels. Moreover, numerical results concerning water density, dielectric permittivity, void volume, and steric energy provide useful details to study
Dupuis, Alexandre; Chatelain, Philippe; Koumoutsakos, Petros
2008-04-01
We present a lattice-Boltzmann method coupled with an immersed boundary technique for the simulation of bluff body flows. The lattice-Boltzmann method for the modeling of the Navier-Stokes equations, is enhanced by a forcing term to account for the no-slip boundary condition on a non-grid conforming boundary. We investigate two alternatives of coupling the boundary forcing term with the grid nodes, namely the direct and the interpolated forcing techniques. The present LB-IB methods are validated in simulations of the incompressible flow past an impulsively started cylinder at low and moderate Reynolds numbers. We present diagnostics such as the near wall vorticity field and the drag coefficient and comparisons with previous computational and experimental works and assess the advantages and drawbacks of the two techniques.
Molaeimanesh, Gholam Reza; Akbari, Mohammad Hadi [Shiraz University, Shiraz (Iran, Islamic Republic of)
2015-03-15
A pore-scale model based on the lattice Boltzmann method (LBM) is proposed for the cathode electrode of a PEM fuel cell with heterogeneous and anisotropic porous gas diffusion layer (GDL) and interdigitated flow field. An active approach is implemented to model multi-component transport in GDL, which leads to enhanced accuracy, especially at higher activation over-potentials. The core of the paper is the implementation of an electrochemical reaction with an active approach in a multi-component lattice Boltzmann model for the first time. After model validation, the capability of the presented model is demonstrated through a parametric study. Effects of activation over-potential, pressure differential between inlet and outlet gas channels, land width to channel width ratio, and channel width are investigated. The results show the significant influence of GDL microstructure on the oxygen distribution and current density profile.
Giona, Massimiliano; Brasiello, Antonio; Crescitelli, Silvestro
2017-08-01
This third part extends the theory of Generalized Poisson-Kac (GPK) processes to nonlinear stochastic models and to a continuum of states. Nonlinearity is treated in two ways: (i) as a dependence of the parameters (intensity of the stochastic velocity, transition rates) of the stochastic perturbation on the state variable, similarly to the case of nonlinear Langevin equations, and (ii) as the dependence of the stochastic microdynamic equations of motion on the statistical description of the process itself (nonlinear Fokker-Planck-Kac models). Several numerical and physical examples illustrate the theory. Gathering nonlinearity and a continuum of states, GPK theory provides a stochastic derivation of the nonlinear Boltzmann equation, furnishing a positive answer to the Kac’s program in kinetic theory. The transition from stochastic microdynamics to transport theory within the framework of the GPK paradigm is also addressed.
Instability theory of the Navier-Stokes-Poisson equations
Jang, Juhi
2011-01-01
The stability question of the Lane-Emden stationary gaseous star configurations is an interesting problem arising in astrophysics. We establish both linear and nonlinear dynamical instability results for the Lane-Emden solutions in the framework of the Navier-Stokes-Poisson system with adiabatic exponent $6/5 < \\gamma < 4/3$.
Large time behavior of Euler-Poisson system for semiconductor
2008-01-01
In this note,we present a framework for the large time behavior of general uniformly bounded weak entropy solutions to the Cauchy problem of Euler-Poisson system of semiconductor devices.It is shown that the solutions converges to the stationary solutions exponentially in time.No smallness and regularity conditions are assumed.
Tailoring graphene to achieve negative Poisson's ratio properties.
Grima, Joseph N; Winczewski, Szymon; Mizzi, Luke; Grech, Michael C; Cauchi, Reuben; Gatt, Ruben; Attard, Daphne; Wojciechowski, Krzysztof W; Rybicki, Jarosław
2015-02-25
Graphene can be made auxetic through the introduction of vacancy defects. This results in the thinnest negative Poisson's ratio material at ambient conditions known so far, an effect achieved via a nanoscale de-wrinkling mechanism that mimics the behavior at the macroscale exhibited by a crumpled sheet of paper when stretched.
Stability of Schr(o)dinger-Poisson type equations
Juan HUANG; Jian ZHANG; Guang-gan CHEN
2009-01-01
Variational methods are used to study the nonlinear Schr(o)dinger-Poisson type equations which model the electromagnetic wave propagating in the plasma in physics. By analyzing the Halniltonian property to construct a constrained variational problem, the existence of the ground state of the system is obtained. Furthermore, it is shown that the ground state is orbitally stable.
On supermatrix models, Poisson geometry, and noncommutative supersymmetric gauge theories
Klimčík, Ctirad [Aix Marseille Université, CNRS, Centrale Marseille I2M, UMR 7373, 13453 Marseille (France)
2015-12-15
We construct a new supermatrix model which represents a manifestly supersymmetric noncommutative regularisation of the UOSp(2|1) supersymmetric Schwinger model on the supersphere. Our construction is much simpler than those already existing in the literature and it was found by using Poisson geometry in a substantial way.
Quantum Poisson-Lie T-duality and WZNW model
Alekseev, A Yu; Tseytlin, Arkady A
1996-01-01
A pair of conformal sigma models related by Poisson-Lie T-duality is constructed by starting with the O(2,2) Drinfeld double. The duality relates the standard SL(2,R) WZNW model to a constrained sigma model defined on SL(2,R) group space. The quantum equivalence of the models is established by using a path integral argument.
Modeling corporate defaults: Poisson autoregressions with exogenous covariates (PARX)
Agosto, Arianna; Cavaliere, Guiseppe; Kristensen, Dennis
We develop a class of Poisson autoregressive models with additional covariates (PARX) that can be used to model and forecast time series of counts. We establish the time series properties of the models, including conditions for stationarity and existence of moments. These results are in turn used...
A Poisson type formula for Hardy classes on Heisenberg's group
Lopushansky O.V.
2010-06-01
Full Text Available The Hardy type class of complex functions with infinite many variables defined on the Schrodinger irreducible unitary orbit of reduced Heisenberg group, generated by the Gauss density, is investigated. A Poisson integral type formula for their analytic extensions on an open ball is established. Taylor coefficients for analytic extensions are described by the associatedsymmetric Fock space.
An application of the Autoregressive Conditional Poisson (ACP) model
Holloway, Jennifer P
2010-11-01
Full Text Available When modelling count data that comes in the form of a time series, the static Poisson regression and standard time series models are often not appropriate. A current study therefore involves the evaluation of several observation-driven and parameter...
Optimality of Poisson Processes Intensity Learning with Gaussian Processes
Kirichenko, A.; van Zanten, H.
2015-01-01
In this paper we provide theoretical support for the so-called "Sigmoidal Gaussian Cox Process" approach to learning the intensity of an inhomogeneous Poisson process on a d-dimensional domain. This method was proposed by Adams, Murray and MacKay (ICML, 2009), who developed a tractable computational
On global solutions for the Vlasov-Poisson system
Peter E. Zhidkov
2004-04-01
Full Text Available In this article we show that the Vlasov-Poisson system has a unique weak solution in the space $L_1cap L_infty$. For this purpose, we use the method of characteristics, unlike the approach in [12].
Optimality of Poisson Processes Intensity Learning with Gaussian Processes
A. Kirichenko; H. van Zanten
2015-01-01
In this paper we provide theoretical support for the so-called "Sigmoidal Gaussian Cox Process" approach to learning the intensity of an inhomogeneous Poisson process on a d-dimensional domain. This method was proposed by Adams, Murray and MacKay (ICML, 2009), who developed a tractable computational
Nonparametric Bayesian inference for multidimensional compound Poisson processes
S. Gugushvili; F. van der Meulen; P. Spreij
2015-01-01
Given a sample from a discretely observed multidimensional compound Poisson process, we study the problem of nonparametric estimation of its jump size density r0 and intensity λ0. We take a nonparametric Bayesian approach to the problem and determine posterior contraction rates in this context, whic
Using the Gamma-Poisson Model to Predict Library Circulations.
Burrell, Quentin L.
1990-01-01
Argues that the gamma mixture of Poisson processes, for all its perceived defects, can be used to make predictions regarding future library book circulations of a quality adequate for general management requirements. The use of the model is extensively illustrated with data from two academic libraries. (Nine references) (CLB)
Poisson processes on groups and Feynamn path integrals
Combe, P.; Rodriguez, R.; Sirugue, M.; Sirugue-Collin, M.; Hoegh-Krohn, R.
1980-10-01
We give an expression for the perturbed evolution of a free evolution by gentle, possibly velocity dependent, potential, in terms of the expectation with respect to a Poisson process on a group. Various applications are given in particular to usual quantum mechanics but also to Fermi and spin systems.
Poisson processes on groups and Feynman path integrals
Combe, Ph.; Høegh-Krohn, R.; Rodriguez, R.; Sirugue, M.; Sirugue-Collin, M.
1980-10-01
We give an expression for the perturbed evolution of a free evolution by gentle, possibly velocity dependent, potential, in terms of the expectation with respect to a Poisson process on a group. Various applications are given in particular to usual quantum mechanics but also to Fermi and spin systems.
Wide-area traffic: The failure of Poisson modeling
Paxson, V.; Floyd, S.
1994-08-01
Network arrivals are often modeled as Poisson processes for analytic simplicity, even though a number of traffic studies have shown that packet interarrivals are not exponentially distributed. The authors evaluate 21 wide-area traces, investigating a number of wide-area TCP arrival processes (session and connection arrivals, FTPDATA connection arrivals within FTP sessions, and TELNET packet arrivals) to determine the error introduced by modeling them using Poisson processes. The authors find that user-initiated TCP session arrivals, such as remote-login and file-transfer, are well-modeled as Poisson processes with fixed hourly rates, but that other connection arrivals deviate considerably from Poisson; that modeling TELNET packet interarrivals as exponential grievously underestimates the burstiness of TELNET traffic, but using the empirical Tcplib[DJCME92] interarrivals preserves burstiness over many time scales; and that FTPDATA connection arrivals within FTP sessions come bunched into ``connection bursts``, the largest of which are so large that they completely dominate FTPDATA traffic. Finally, they offer some preliminary results regarding how the findings relate to the possible self-similarity of wide-area traffic.
Characterization and global analysis of a family of Poisson structures
Hernandez-Bermejo, Benito [Escuela Superior de Ciencias Experimentales y Tecnologia, Edificio Departamental II, Universidad Rey Juan Carlos, Calle Tulipan S/N, 28933 (Mostoles), Madrid (Spain)]. E-mail: benito.hernandez@urjc.es
2006-06-26
A three-dimensional family of solutions of the Jacobi equations for Poisson systems is characterized. In spite of its general form it is possible the explicit and global determination of its main features, such as the symplectic structure and the construction of the Darboux canonical form. Examples are given.
Wavelet-based Poisson rate estimation using the Skellam distribution
Hirakawa, Keigo; Baqai, Farhan; Wolfe, Patrick J.
2009-02-01
Owing to the stochastic nature of discrete processes such as photon counts in imaging, real-world data measurements often exhibit heteroscedastic behavior. In particular, time series components and other measurements may frequently be assumed to be non-iid Poisson random variables, whose rate parameter is proportional to the underlying signal of interest-witness literature in digital communications, signal processing, astronomy, and magnetic resonance imaging applications. In this work, we show that certain wavelet and filterbank transform coefficients corresponding to vector-valued measurements of this type are distributed as sums and differences of independent Poisson counts, taking the so-called Skellam distribution. While exact estimates rarely admit analytical forms, we present Skellam mean estimators under both frequentist and Bayes models, as well as computationally efficient approximations and shrinkage rules, that may be interpreted as Poisson rate estimation method performed in certain wavelet/filterbank transform domains. This indicates a promising potential approach for denoising of Poisson counts in the above-mentioned applications.
Determining Planetary Temperatures with the Stefan-Boltzmann Law
LoPresto, Michael C.; Hagoort, Nichole
2011-01-01
What follows is a description of several activities involving the Stefan-Boltzmann radiation law that can provide laboratory experience beyond what is normally found in traditional introductory thermodynamics experiments on thermal expansion, specific heat, and heats of transformation. The activities also provide more extensive coverage of and…
Determining Planetary Temperatures with the Stefan-Boltzmann Law
LoPresto, Michael C.; Hagoort, Nichole
2011-01-01
What follows is a description of several activities involving the Stefan-Boltzmann radiation law that can provide laboratory experience beyond what is normally found in traditional introductory thermodynamics experiments on thermal expansion, specific heat, and heats of transformation. The activities also provide more extensive coverage of and…
An efficient learning procedure for deep Boltzmann machines.
Salakhutdinov, Ruslan; Hinton, Geoffrey
2012-08-01
We present a new learning algorithm for Boltzmann machines that contain many layers of hidden variables. Data-dependent statistics are estimated using a variational approximation that tends to focus on a single mode, and data-independent statistics are estimated using persistent Markov chains. The use of two quite different techniques for estimating the two types of statistic that enter into the gradient of the log likelihood makes it practical to learn Boltzmann machines with multiple hidden layers and millions of parameters. The learning can be made more efficient by using a layer-by-layer pretraining phase that initializes the weights sensibly. The pretraining also allows the variational inference to be initialized sensibly with a single bottom-up pass. We present results on the MNIST and NORB data sets showing that deep Boltzmann machines learn very good generative models of handwritten digits and 3D objects. We also show that the features discovered by deep Boltzmann machines are a very effective way to initialize the hidden layers of feedforward neural nets, which are then discriminatively fine-tuned.
Boltzmann-type control of opinion consensus through leaders.
Albi, G; Pareschi, L; Zanella, M
2014-11-13
The study of formations and dynamics of opinions leading to the so-called opinion consensus is one of the most important areas in mathematical modelling of social sciences. Following the Boltzmann-type control approach recently introduced by the first two authors, we consider a group of opinion leaders who modify their strategy accordingly to an objective functional with the aim of achieving opinion consensus. The main feature of the Boltzmann-type control is that, owing to an instantaneous binary control formulation, it permits the minimization of the cost functional to be embedded into the microscopic leaders' interactions of the corresponding Boltzmann equation. The related Fokker-Planck asymptotic limits are also derived, which allow one to give explicit expressions of stationary solutions. The results demonstrate the validity of the Boltzmann-type control approach and the capability of the leaders' control to strategically lead the followers' opinion. © 2014 The Author(s) Published by the Royal Society. All rights reserved.
The peeling process of infinite Boltzmann planar maps
Budd, Timothy George
2016-01-01
criterion has a very simple interpretation. The finite random planar maps under consideration were recently proved to possess a well-defined local limit known as the infinite Boltzmann planar map (IBPM). Inspired by recent work of Curien and Le Gall, we show that the peeling process on the IBPM can...
Lattice Boltzmann method for linear oscillatory noncontinuum flows.
Shi, Yong; Yap, Ying Wan; Sader, John E
2014-03-01
Oscillatory gas flows are commonly generated by micro- and nanoelectromechanical systems. Due to their small size and high operating frequencies, these devices often produce noncontinuum gas flows. Theoretical analysis of such flows requires solution of the unsteady Boltzmann equation, which can present a formidable challenge. In this article, we explore the applicability of the lattice Boltzmann (LB) method to such linear oscillatory noncontinuum flows; this method is derived from the linearized Boltzmann Bhatnagar-Gross-Krook (BGK) equation. We formulate four linearized LB models in the frequency domain, based on Gaussian-Hermite quadratures of different algebraic precision (AP). The performance of each model is assessed by comparison to high-accuracy numerical solutions to the linearized Boltzmann-BGK equation for oscillatory Couette flow. The numerical results demonstrate that high even-order LB models provide superior performance over the greatest noncontinuum range. Our results also highlight intrinsic deficiencies in the current LB framework, which is incapable of capturing noncontinuum behavior at high oscillation frequencies, regardless of quadrature AP and the Knudsen number.
Lattice Boltzmann method for linear oscillatory noncontinuum flows
Shi, Yong; Yap, Ying Wan; Sader, John E.
2014-03-01
Oscillatory gas flows are commonly generated by micro- and nanoelectromechanical systems. Due to their small size and high operating frequencies, these devices often produce noncontinuum gas flows. Theoretical analysis of such flows requires solution of the unsteady Boltzmann equation, which can present a formidable challenge. In this article, we explore the applicability of the lattice Boltzmann (LB) method to such linear oscillatory noncontinuum flows; this method is derived from the linearized Boltzmann Bhatnagar-Gross-Krook (BGK) equation. We formulate four linearized LB models in the frequency domain, based on Gaussian-Hermite quadratures of different algebraic precision (AP). The performance of each model is assessed by comparison to high-accuracy numerical solutions to the linearized Boltzmann-BGK equation for oscillatory Couette flow. The numerical results demonstrate that high even-order LB models provide superior performance over the greatest noncontinuum range. Our results also highlight intrinsic deficiencies in the current LB framework, which is incapable of capturing noncontinuum behavior at high oscillation frequencies, regardless of quadrature AP and the Knudsen number.
A Parallel Lattice Boltzmann Model of a Carotid Artery
Boyd, J.; Ryan, S. J.; Buick, J. M.
2008-11-01
A parallel implementation of the lattice Boltzmann model is considered for a three dimensional model of the carotid artery. The computational method and its parallel implementation are described. The performance of the parallel implementation on a Beowulf cluster is presented, as are preliminary hemodynamic results.
Analytical solutions of the lattice Boltzmann BGK model
Zou, Q; Doolen, G D; Zou, Qisu; Hou, Shuling; Doolen, Gary D.
1995-01-01
Abstract: Analytical solutions of the two dimensional triangular and square lattice Boltzmann BGK models have been obtained for the plain Poiseuille flow and the plain Couette flow. The analytical solutions are written in terms of the characteristic velocity of the flow, the single relaxation time representation of these two flows without any approximation.
Generalized Relativistic Chapman-Enskog Solution of the Boltzmann Equation
García-Perciante, A L; García-Colin, L S
2007-01-01
The Chapman-Enskog method of solution of the relativistic Boltzmann equation is generalized in order to admit a time-derivative term associated to the thermodynamic force in its first order solution. Both existence and uniqueness of such a solution are proved based on the standard theory of integral equations. The mathematical implications of the generalization here introduced are briefly explored.
Nonequilibrium phenomena in QCD and BEC. Boltzmann and beyond
Stockamp, T.
2006-12-22
In chapter 2 we chose the real time formalism to discuss some basic principles in quantum field theory at finite temperature. This enables us to derive the quantum Boltzmann equation from the Schwinger-Dyson series. We then shortly introduce the basic concepts of QCD which are needed to understand the physics of QGP formation. After a detailed account on the bottom-up scenario we show the consistency of this approach by a diagramatical analysis of the relevant Boltzmann collision integrals. Chapter 3 deals with BEC dynamics out of equilibrium. After an introduction to the fundamental theoretical tool - namely the Gross-Pitaevskii equation - we focus on a generalization to finite temperature developed by Zaremba, Nikuni and Griffin (ZNG). These authors use a Boltzmann equation to describe the interactions between condensed and excited atoms and manage in this way to describe condensate growth. We then turn to a discussion on the 2PI effective action and derive equations of motion for a relativistic scalar field theory. In the nonrelativistic limit these equations are shown to coincide with the ZNG theory when a quasiparticle approximation is applied. Finally, we perform a numerical analysis of the full 2PI equations. These remain valid even at strong coupling and far from equilibrium, and thus go far beyond Boltzmann's approach. For simplicity, we limit ourselves to a homogeneous system and present the first 3+1 dimensional study of condensate melting. (orig.)
Metamaterial characterization using Boltzmann's kinetic equation for electrons
Novitsky, Andrey; Zhukovsky, Sergei; Novitsky, D.
2013-01-01
Statistical properties of electrons in metals are taken into consideration to describe the microscopic motion of electrons. Assuming degenerate electron gas in metal, we introduce the Boltzmann kinetic equation to supplement Maxwell's equations. The solution of these equations clearly shows the r...
Numerical solution of Boltzmann's equation
Sod, G.A.
1976-04-01
The numerical solution of Boltzmann's equation is considered for a gas model consisting of rigid spheres by means of Hilbert's expansion. If only the first two terms of the expansion are retained, Boltzmann's equation reduces to the Boltzmann-Hilbert integral equation. Successive terms in the Hilbert expansion are obtained by solving the same integral equation with a different source term. The Boltzmann-Hilbert integral equation is solved by a new very fast numerical method. The success of the method rests upon the simultaneous use of four judiciously chosen expansions; Hilbert's expansion for the distribution function, another expansion of the distribution function in terms of Hermite polynomials, the expansion of the kernel in terms of the eigenvalues and eigenfunctions of the Hilbert operator, and an expansion involved in solving a system of linear equations through a singular value decomposition. The numerical method is applied to the study of the shock structure in one space dimension. Numerical results are presented for Mach numbers of 1.1 and 1.6. 94 refs, 7 tables, 1 fig.
The lattice Boltzmann method and the problem of turbulence
Djenidi, L. [School of Engineering The University of Newcastle, Callaghan NSW 2308 (Australia)
2015-03-10
This paper reports a brief review of numerical simulations of homogeneous isotopic turbulence (HIT) using the lattice Boltzmann method (LBM). The LBM results shows that the details of HIT are well captured and in agreement with existing data. This clearly indicates that the LBM is as good as current Navier-Stokes solvers and is very much adequate for investigating the problem of turbulence.
Measuring Boltzmann's Constant with Carbon Dioxide
Ivanov, Dragia; Nikolov, Stefan
2013-01-01
In this paper we present two experiments to measure Boltzmann's constant--one of the fundamental constants of modern-day physics, which lies at the base of statistical mechanics and thermodynamics. The experiments use very basic theory, simple equipment and cheap and safe materials yet provide very precise results. They are very easy and…
EXTERNAL BODY FORCE IN FINITE DIFFERENCE LATTICE BOLTZMANN METHOD
CHEN Sheng; LIU Zhao-hui; SHI Bao-chang; ZHENG Chu-guang
2005-01-01
A new finite difference lattice Boltzmann scheme is developed. Because of analyzing the influence of external body force roundly, the correct Navier-Stokes equations with the external body force are recovered, without any additional unphysical terms. And some numerical results are presented. The result which close agreement with analytical data shows the good performance of the model.
Lattice Boltzmann simulations of droplet formation during microchannel emulsification
Zwan, van der E.A.; Sman, van der R.G.M.; Schroën, C.G.P.H.; Boom, R.M.
2009-01-01
In this study, we compared microchannel droplet formation in a microfluidics device with a two phase lattice Boltzmann simulation. The droplet formation was found to be qualitatively described, with a slightly smaller droplet in the simulation. This was due to the finite thickness of the interface i
Performance evaluation of a parallel sparse lattice Boltzmann solver
Axner, L.; Bernsdorf, J.; Zeiser, T.; Lammers, P.; Linxweiler, J.; Hoekstra, A.G.
2008-01-01
We develop a performance prediction model for a parallelized sparse lattice Boltzmann solver and present performance results for simulations of flow in a variety of complex geometries. A special focus is on partitioning and memory/load balancing strategy for geometries with a high solid fraction and
Measuring Boltzmann's Constant with Carbon Dioxide
Ivanov, Dragia; Nikolov, Stefan
2013-01-01
In this paper we present two experiments to measure Boltzmann's constant--one of the fundamental constants of modern-day physics, which lies at the base of statistical mechanics and thermodynamics. The experiments use very basic theory, simple equipment and cheap and safe materials yet provide very precise results. They are very easy and…
Distribution Learning in Evolutionary Strategies and Restricted Boltzmann Machines
Krause, Oswin
The thesis is concerned with learning distributions in the two settings of Evolutionary Strategies (ESs) and Restricted Boltzmann Machines (RBMs). In both cases, the distributions are learned from samples, albeit with different goals. Evolutionary Strategies are concerned with finding an optimum ...
Thermal creep problems by the discrete Boltzmann equation
L. Preziosi
1991-05-01
Full Text Available This paper deals with an initial-boundary value problem for the discrete Boltzmann equation confined between two moving walls at different temperature. A model suitable for the quantitative analysis of the initial boundary value problem and the relative existence theorem are given.
Poisson Regression Analysis of Illness and Injury Surveillance Data
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 due 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
A fast iterative scheme for the linearized Boltzmann equation
Wu, Lei; Zhang, Jun; Liu, Haihu; Zhang, Yonghao; Reese, Jason M.
2017-06-01
Iterative schemes to find steady-state solutions to the Boltzmann equation are efficient for highly rarefied gas flows, but can be very slow to converge in the near-continuum flow regime. In this paper, a synthetic iterative scheme is developed to speed up the solution of the linearized Boltzmann equation by penalizing the collision operator L into the form L = (L + Nδh) - Nδh, where δ is the gas rarefaction parameter, h is the velocity distribution function, and N is a tuning parameter controlling the convergence rate. The velocity distribution function is first solved by the conventional iterative scheme, then it is corrected such that the macroscopic flow velocity is governed by a diffusion-type equation that is asymptotic-preserving into the Navier-Stokes limit. The efficiency of this new scheme is assessed by calculating the eigenvalue of the iteration, as well as solving for Poiseuille and thermal transpiration flows. We find that the fastest convergence of our synthetic scheme for the linearized Boltzmann equation is achieved when Nδ is close to the average collision frequency. The synthetic iterative scheme is significantly faster than the conventional iterative scheme in both the transition and the near-continuum gas flow regimes. Moreover, due to its asymptotic-preserving properties, the synthetic iterative scheme does not need high spatial resolution in the near-continuum flow regime, which makes it even faster than the conventional iterative scheme. Using this synthetic scheme, with the fast spectral approximation of the linearized Boltzmann collision operator, Poiseuille and thermal transpiration flows between two parallel plates, through channels of circular/rectangular cross sections and various porous media are calculated over the whole range of gas rarefaction. Finally, the flow of a Ne-Ar gas mixture is solved based on the linearized Boltzmann equation with the Lennard-Jones intermolecular potential for the first time, and the difference
Lattice Boltzmann simulations of turbulent shear flow between parallel porous walls
唐政; 刘难生; 董宇红
2014-01-01
The effects of two parallel porous walls are investigated, consisting of the Darcy number and the porosity of a porous medium, on the behavior of turbulent shear flows as well as skin-friction drag. The turbulent channel flow with a porous surface is directly simulated by the lattice Boltzmann method (LBM). The Darcy-Brinkman-Forcheimer (DBF) acting force term is added in the lattice Boltzmann equation to simu-late the turbulent flow bounded by porous walls. It is found that there are two opposite trends (enhancement or reduction) for the porous medium to modify the intensities of the velocity fluctuations and the Reynolds stresses in the near wall region. The parametric study shows that flow modification depends on the Darcy number and the porosity of the porous medium. The results show that, with respect to the conventional impermeable wall, the degree of turbulence modification does not depend on any simple set of param-eters obviously. Moreover, the drag in porous wall-bounded turbulent flow decreases if the Darcy number is smaller than the order of O(10−4) and the porosity of porous walls is up to 0.4.
Stochastic poisson equations associated to lie algebroids and some refinements of a principal bundle
Ivan, Gheorghe
2010-01-01
The aim of this paper is to present the stochastic Poisson equations associated to Lie algebroids. The stochastic Poisson equations associated to a refinement of a concrete principal bundle are determined.
Noncommutative Poisson structures, derived representation schemes and Calabi-Yau algebras
Berest, Yuri; Eshmatov, Farkhod; Ramadoss, Ajay
2012-01-01
Recantly, William Crawley-Boevey proposed the definition of a Poisson structure on a noncommutative algebra $A$ based on the Kontsevich principle. His idea was to find the {\\it weakest} possible structure on $A$ that induces standard (commutative) Poisson structures on all representation spaces $ \\Rep_V(A) $. It turns out that such a weak Poisson structure on $A$ is a Lie algebra bracket on the 0-th cyclic homology $ \\HC_0(A) $ satisfying some extra conditions; it was thus called in an {\\it $ H_0$-Poisson structure}. This paper studies a higher homological extension of this construction. In our more general setting, we show that noncommutative Poisson structures in the above sense behave nicely with respect to homotopy (in the sense that homotopy equivalent NC Poisson structures on $A$ induce (via the derived representation functor) homotopy equivalent Poisson algebra structures on the derved representation schemes $\\DRep_V(A) $). For an ordinary algebra $A$, a noncommutative Poisson structure on a semifree (...
2D sigma models and differential Poisson algebras
Arias, Cesar; Boulanger, Nicolas; Sundell, Per; Torres-Gomez, Alexander
2015-08-01
We construct a two-dimensional topological sigma model whose target space is endowed with a Poisson algebra for differential forms. The model consists of an equal number of bosonic and fermionic fields of worldsheet form degrees zero and one. The action is built using exterior products and derivatives, without any reference to a worldsheet metric, and is of the covariant Hamiltonian form. The equations of motion define a universally Cartan integrable system. In addition to gauge symmetries, the model has one rigid nilpotent supersymmetry corresponding to the target space de Rham operator. The rigid and local symmetries of the action, respectively, are equivalent to the Poisson bracket being compatible with the de Rham operator and obeying graded Jacobi identities. We propose that perturbative quantization of the model yields a covariantized differential star product algebra of Kontsevich type. We comment on the resemblance to the topological A model.
2D sigma models and differential Poisson algebras
Arias, Cesar; Sundell, Per; Torres-Gomez, Alexander
2015-01-01
We construct a two-dimensional topological sigma model whose target space is endowed with a Poisson algebra for differential forms. The model consists of an equal number of bosonic and fermionic fields of worldsheet form degrees zero and one. The action is built using exterior products and derivatives, without any reference to any worldsheet metric, and is of the covariant Hamiltonian form. The equations of motion define a universally Cartan integrable system. In addition to gauge symmetries, the model has one rigid nilpotent supersymmetry corresponding to the target space de Rham operator. The rigid and local symmetries of the action, respectively, are equivalent to the Poisson bracket being compatible with the de Rham operator and obeying graded Jacobi identities. We propose that perturbative quantization of the model yields a covariantized differential star product algebra of Kontsevich type. We comment on the resemblance to the topological A model.
A COMPOUND POISSON MODEL FOR LEARNING DISCRETE BAYESIAN NETWORKS
Abdelaziz GHRIBI; Afif MASMOUDI
2013-01-01
We introduce here the concept of Bayesian networks, in compound Poisson model, which provides a graphical modeling framework that encodes the joint probability distribution for a set of random variables within a directed acyclic graph. We suggest an approach proposal which offers a new mixed implicit estimator. We show that the implicit approach applied in compound Poisson model is very attractive for its ability to understand data and does not require any prior information. A comparative study between learned estimates given by implicit and by standard Bayesian approaches is established. Under some conditions and based on minimal squared error calculations, we show that the mixed implicit estimator is better than the standard Bayesian and the maximum likelihood estimators. We illustrate our approach by considering a simulation study in the context of mobile communication networks.
2D sigma models and differential Poisson algebras
Arias, Cesar [Departamento de Ciencias Físicas, Universidad Andres Bello,Republica 220, Santiago (Chile); Boulanger, Nicolas [Service de Mécanique et Gravitation, Université de Mons - UMONS,20 Place du Parc, 7000 Mons (Belgium); Laboratoire de Mathématiques et Physique Théorique,Unité Mixte de Recherche 7350 du CNRS, Fédération de Recherche 2964 Denis Poisson,Université François Rabelais, Parc de Grandmont, 37200 Tours (France); Sundell, Per [Departamento de Ciencias Físicas, Universidad Andres Bello,Republica 220, Santiago (Chile); Torres-Gomez, Alexander [Departamento de Ciencias Físicas, Universidad Andres Bello,Republica 220, Santiago (Chile); Instituto de Ciencias Físicas y Matemáticas, Universidad Austral de Chile-UACh,Valdivia (Chile)
2015-08-18
We construct a two-dimensional topological sigma model whose target space is endowed with a Poisson algebra for differential forms. The model consists of an equal number of bosonic and fermionic fields of worldsheet form degrees zero and one. The action is built using exterior products and derivatives, without any reference to a worldsheet metric, and is of the covariant Hamiltonian form. The equations of motion define a universally Cartan integrable system. In addition to gauge symmetries, the model has one rigid nilpotent supersymmetry corresponding to the target space de Rham operator. The rigid and local symmetries of the action, respectively, are equivalent to the Poisson bracket being compatible with the de Rham operator and obeying graded Jacobi identities. We propose that perturbative quantization of the model yields a covariantized differential star product algebra of Kontsevich type. We comment on the resemblance to the topological A model.
Reference manual for the POISSON/SUPERFISH Group of Codes
1987-01-01
The POISSON/SUPERFISH Group codes were set up to solve two separate problems: the design of magnets and the design of rf cavities in a two-dimensional geometry. The first stage of either problem is to describe the layout of the magnet or cavity in a way that can be used as input to solve the generalized Poisson equation for magnets or the Helmholtz equations for cavities. The computer codes require that the problems be discretized by replacing the differentials (dx,dy) by finite differences ({delta}X,{delta}Y). Instead of defining the function everywhere in a plane, the function is defined only at a finite number of points on a mesh in the plane.
Finite-size effects and percolation properties of Poisson geometries
Larmier, C.; Dumonteil, E.; Malvagi, F.; Mazzolo, A.; Zoia, A.
2016-07-01
Random tessellations of the space represent a class of prototype models of heterogeneous media, which are central in several applications in physics, engineering, and life sciences. In this work, we investigate the statistical properties of d -dimensional isotropic Poisson geometries by resorting to Monte Carlo simulation, with special emphasis on the case d =3 . We first analyze the behavior of the key features of these stochastic geometries as a function of the dimension d and the linear size L of the domain. Then, we consider the case of Poisson binary mixtures, where the polyhedra are assigned two labels with complementary probabilities. For this latter class of random geometries, we numerically characterize the percolation threshold, the strength of the percolating cluster, and the average cluster size.
Poisson Sigma Model with branes and hyperelliptic Riemann surfaces
Ferrario, Andrea
2007-01-01
We derive the explicit form of the superpropagators in presence of general boundary conditions (coisotropic branes) for the Poisson Sigma Model. This generalizes the results presented in Cattaneo and Felder's previous works for the Kontsevich angle function used in the deformation quantization program of Poisson manifolds without branes or with at most two branes. The relevant superpropagators for n branes are defined as gauge fixed homotopy operators of a complex of differential forms on n sided polygons P_n with particular "alternating" boundary conditions. In presence of more than three branes we use first order Riemann theta functions with odd singular characteristics on the Jacobian variety of a hyperelliptic Riemann surface (canonical setting). In genus g the superpropagators present g zero modes contributions.
The Schr\\"odinger-Poisson system on the sphere
Gérard, Patrick
2010-01-01
We study the Schr\\"odinger-Poisson system on the unit sphere $\\SS^2$ of $\\RR^3$, modeling the quantum transport of charged particles confined on a sphere by an external potential. Our first results concern the Cauchy problem for this system. We prove that this problem is regularly well-posed on every $H^s(\\SS ^2)$ with $s>0$, and not uniformly well-posed on $L^2(\\SS ^2)$. The proof of well-posedness relies on multilinear Strichartz estimates, the proof of ill-posedness relies on the construction of a counterexample which concentrates exponentially on a closed geodesic. In a second part of the paper, we prove that this model can be obtained as the limit of the three dimensional Schr\\"odinger-Poisson system, singularly perturbed by an external potential that confines the particles in the vicinity of the sphere.
Histogram bin width selection for time-dependent Poisson processes
Koyama, Shinsuke; Shinomoto, Shigeru [Department of Physics, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502 (Japan)
2004-07-23
In constructing a time histogram of the event sequences derived from a nonstationary point process, we wish to determine the bin width such that the mean squared error of the histogram from the underlying rate of occurrence is minimized. We find that the optimal bin widths obtained for a doubly stochastic Poisson process and a sinusoidally regulated Poisson process exhibit different scaling relations with respect to the number of sequences, time scale and amplitude of rate modulation, but both diverge under similar parametric conditions. This implies that under these conditions, no determination of the time-dependent rate can be made. We also apply the kernel method to these point processes, and find that the optimal kernels do not exhibit any critical phenomena, unlike the time histogram method.
Probability distributions for Poisson processes with pile-up
Sevilla, Diego J R
2013-01-01
In this paper, two parametric probability distributions capable to describe the statistics of X-ray photon detection by a CCD are presented. They are formulated from simple models that account for the pile-up phenomenon, in which two or more photons are counted as one. These models are based on the Poisson process, but they have an extra parameter which includes all the detailed mechanisms of the pile-up process that must be fitted to the data statistics simultaneously with the rate parameter. The new probability distributions, one for number of counts per time bins (Poisson-like), and the other for waiting times (exponential-like) are tested fitting them to statistics of real data, and between them through numerical simulations, and their results are analyzed and compared. The probability distributions presented here can be used as background statistical models to derive likelihood functions for statistical methods in signal analysis.
A fast unbinned test on event clustering in Poisson processes
Prahl, J
1999-01-01
An unbinned statistical test on cluster-like deviations from Poisson processes for point process data is introduced, presented in the context of time variability analysis of astrophysical sources in count rate experiments. The measure of deviation of the actually obtained temporal event distribution from that of a Poisson process is derived from the distribution of time differences between two consecutive events in a natural way. The differential character of the measure suggests this test in particular for the search of irregular burst-like structures in experimental data. The construction allows the application of the test even for very low event numbers. Furthermore, the test can easily be applied in the case of varying acceptance of the detector as well. The simple and direct use of background events simultaneously acquired under the same conditions to account for acceptance variations is possible, allowing for easy application especially in earth-bound gamma-ray experiments. Central features are the fast...
Histogram bin width selection for time-dependent Poisson processes
Koyama, Shinsuke; Shinomoto, Shigeru
2004-07-01
In constructing a time histogram of the event sequences derived from a nonstationary point process, we wish to determine the bin width such that the mean squared error of the histogram from the underlying rate of occurrence is minimized. We find that the optimal bin widths obtained for a doubly stochastic Poisson process and a sinusoidally regulated Poisson process exhibit different scaling relations with respect to the number of sequences, time scale and amplitude of rate modulation, but both diverge under similar parametric conditions. This implies that under these conditions, no determination of the time-dependent rate can be made. We also apply the kernel method to these point processes, and find that the optimal kernels do not exhibit any critical phenomena, unlike the time histogram method.
Poisson structures in BRST-antiBRST invariant Lagrangian formalism
Geyer, B; Nersessian, A P; Geyer, Bodo; Lavrov, Petr; Nersessian, Armen
2001-01-01
We show that the specific operators V^a appearing in the triplectic formalism can be viewed as the anti-Hamiltonian vector fields generated by a second rank irreducible Sp(2) tensor. This allows for an explicit realization of the triplectic algebra being constructed from an arbitrary Poisson bracket on the space of the fields only. We show that the whole space of fields and antifields can be equipped with an even supersymplectic structure when this Poisson bracket is non-degenerate. This observation opens the possibility to provide the BRST/antiBRST path integral by a well-defined integration measure, as well as to establish a direct link between the Sp(2) symmetric Lagrangian and Hamiltonian BRST quantization schemes.
Critical elements on fitting the Bayesian multivariate Poisson Lognormal model
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.
An adaptive fast multipole accelerated Poisson solver for complex geometries
Askham, T.; Cerfon, A. J.
2017-09-01
We present a fast, direct and adaptive Poisson solver for complex two-dimensional geometries based on potential theory and fast multipole acceleration. More precisely, the solver relies on the standard decomposition of the solution as the sum of a volume integral to account for the source distribution and a layer potential to enforce the desired boundary condition. The volume integral is computed by applying the FMM on a square box that encloses the domain of interest. For the sake of efficiency and convergence acceleration, we first extend the source distribution (the right-hand side in the Poisson equation) to the enclosing box as a C0 function using a fast, boundary integral-based method. We demonstrate on multiply connected domains with irregular boundaries that this continuous extension leads to high accuracy without excessive adaptive refinement near the boundary and, as a result, to an extremely efficient ;black box; fast solver.
Bazzani, A; Franchi, A; Rambaldi, S; Turchetti, G
2005-01-01
We analyze the accuracy of a 2D Poisson-Vlasov PIC integrator, taking the KV as a reference solution for a FODO cell. The particle evolution is symplectic and the Poisson solver is based on FFT. The numerical error, evaluated by comparing the moments of the distribution and the electric field with the exact solution, shows a linear growth. This effect can be modeled by a white noise in the envelope equations for the KV beam. In order to investigate the collisional effects we have integrated the Hamilton's equations for N charged macro-particles with a hard-core r/sub H/ reducing the computational complexity to N/sup 3/2/. In the constant focusing case we observed that a KV beam, matched or mismatched relaxes to the Maxwell-Boltzmann self consistent distribution on a time interval, which depends on r/sub H/ and has a finite limit, for r/sub H/ to 0. A fully 3D PIC code for short bunches was developed for the ADS linac design at LNL (Italy). A 3D particle-core model, based on Langevin's equations with the drift...
Events in time: Basic analysis of Poisson data
Engelhardt, M.E.
1994-09-01
The report presents basic statistical methods for analyzing Poisson data, such as the member of events in some period of time. It gives point estimates, confidence intervals, and Bayesian intervals for the rate of occurrence per unit of time. It shows how to compare subsets of the data, both graphically and by statistical tests, and how to look for trends in time. It presents a compound model when the rate of occurrence varies randomly. Examples and SAS programs are given.
Statistical Tests of the PTHA Poisson Assumption for Submarine Landslides
Geist, E. L.; Chaytor, J. D.; Parsons, T.; Ten Brink, U. S.
2012-12-01
We demonstrate that a sequence of dated mass transport deposits (MTDs) can provide information to statistically test whether or not submarine landslides associated with these deposits conform to a Poisson model of occurrence. Probabilistic tsunami hazard analysis (PTHA) most often assumes Poissonian occurrence for all sources, with an exponential distribution of return times. Using dates that define the bounds of individual MTDs, we first describe likelihood and Monte Carlo methods of parameter estimation for a suite of candidate occurrence models (Poisson, lognormal, gamma, Brownian Passage Time). In addition to age-dating uncertainty, both methods incorporate uncertainty caused by the open time intervals: i.e., before the first and after the last event to the present. Accounting for these open intervals is critical when there are a small number of observed events. The optimal occurrence model is selected according to both the Akaike Information Criteria (AIC) and Akaike's Bayesian Information Criterion (ABIC). In addition, the likelihood ratio test can be performed on occurrence models from the same family: e.g., the gamma model relative to the exponential model of return time distribution. Parameter estimation, model selection, and hypothesis testing are performed on data from two IODP holes in the northern Gulf of Mexico that penetrated a total of 14 MTDs, some of which are correlated between the two holes. Each of these events has been assigned an age based on microfossil zonations and magnetostratigraphic datums. Results from these sites indicate that the Poisson assumption is likely valid. However, parameter estimation results using the likelihood method for one of the sites suggest that the events may have occurred quasi-periodically. Methods developed in this study provide tools with which one can determine both the rate of occurrence and the statistical validity of the Poisson assumption when submarine landslides are included in PTHA.
Dimension free and infinite variance tail estimates on Poisson space
Breton, J. C.; Houdré, C.; Privault, N.
2004-01-01
Concentration inequalities are obtained on Poisson space, for random functionals with finite or infinite variance. In particular, dimension free tail estimates and exponential integrability results are given for the Euclidean norm of vectors of independent functionals. In the finite variance case these results are applied to infinitely divisible random variables such as quadratic Wiener functionals, including L\\'evy's stochastic area and the square norm of Brownian paths. In the infinite vari...
Translated Poisson Mixture Model for Stratification Learning (PREPRINT)
2007-09-01
unclassified b. ABSTRACT unclassified c. THIS PAGE unclassified Translated Poisson Mixture Model for Stratification Learning Gloria Haro Dept. Teoria ...Pless. Figure 1 shows, for each algorithm, the point cloud with each point colored and marked differently according to its classification. In the dif...1: Clustering of a spiral and a plane. Results with different algorithms (this is a color figure). Due to the statistical nature of the R-TPMM
On terminating Poisson processes in some shock models
Finkelstein, Maxim, E-mail: FinkelMI@ufs.ac.z [Department of Mathematical Statistics, University of the Free State, Bloemfontein (South Africa); Max Planck Institute for Demographic Research, Rostock (Germany); Marais, Francois, E-mail: fmarais@csc.co [CSC, Cape Town (South Africa)
2010-08-15
A system subject to a point process of shocks is considered. Shocks occur in accordance with the homogeneous Poisson process. Different criteria of system failure (termination) are discussed and the corresponding probabilities of failure (accident)-free performance are derived. The described analytical approach is based on deriving integral equations for each setting and solving these equations through the Laplace transform. Some approximations are analyzed and further generalizations and applications are discussed.
Generalized Poisson processes in quantum mechanics and field theory
Combe, P.; Rodriguez, R. (Centre National de la Recherche Scientifique, 13 - Marseille (France). Faculte des Sciences de Luminy); Hoegh-Krohn, R.; Sirugue, M.; Sirugue-Collin, M.
1981-11-01
In section 2 we describe more carefully the generalized Poisson processes, giving a realization of the underlying probability space, and we characterize these processes by their characteristic functionals. Section 3 is devoted to the proof of the previous formula for quantum mechanical systems, with possibly velocity dependent potentials and in section 4 we give an application of the previous theory to some relativistic Bose field models.
Experimental dead-time distortions of poisson processes
Faraci, G.; Pennisi, A. R.
1983-07-01
In order to check the distortions, introduced by a non-extended dead time on the Poisson statistics, accurate experiments have been made in single channel counting. At a given measuring time, the dependence on the choice of the time origin and on the width of the dead time has been verified. An excellent agreement has been found between the theoretical expressions and the experimental curves.
Experimental dead-time distortions of Poisson processes
Faraci, G.; Pennisi, A.R. (Catania Univ. (Italy). Ist. di Fisica; Consiglio Nazionale delle Ricerche, Catania (Italy). Gruppo Nazionale di Struttura della Materia)
1983-07-01
In order to check the distortions, introduced by a non-extended dead time on the Poisson statistics, accurate experiments have been made in single channel counting. At a given measuring time, the dependence on the choice of the time origin and on the width of the dead time has been verified. An excellent agreement has been found between the theoretical expressions and the experimental curves.
Comparing Poisson Sigma Model with A-model
Bonechi, F.; Cattaneo, A. S.; Iraso, R.
2016-10-01
We discuss the A-model as a gauge fixing of the Poisson Sigma Model with target a symplectic structure. We complete the discussion in [4], where a gauge fixing defined by a compatible complex structure was introduced, by showing how to recover the A-model hierarchy of observables in terms of the AKSZ observables. Moreover, we discuss the off-shell supersymmetry of the A-model as a residual BV symmetry of the gauge fixed PSM action.
Daisy Models Semi-Poisson statistics and beyond
Hernández-Saldaña, H; Seligman, T H
1999-01-01
Semi-Poisson statistics are shown to be obtained by removing every other number from a random sequence. Retaining every (r+1)th level we obtain a family of secuences which we call daisy models. Their statistical properties coincide with those of Bogomolny's nearest-neighbour interaction Coulomb gas if the inverse temperature coincides with the integer r. In particular the case r=2 reproduces closely the statistics of quasi-optimal solutions of the traveling salesman problem.
Group-buying inventory policy with demand under Poisson process
Tammarat Kleebmek
2016-02-01
Full Text Available The group-buying is the modern business of selling in the uncertain market. With an objective to minimize costs for sellers arising from ordering and reordering, we present in this paper the group buying inventory model, with the demand governed by a Poisson process and the product sale distributed as Binomial distribution. The inventory level is under continuous review, while the lead time is fixed. A numerical example is illustrated.
Decomposition of almost Poisson structure of non-self-adjoint dynamical systems
无
2009-01-01
Non-self-adjoint dynamical systems, e.g., nonholonomic systems, can admit an almost Poisson structure, which is formulated by a kind of Poisson bracket satisfying the usual properties except for the Jacobi identity. A general theory of the almost Poisson structure is investigated based on a decompo- sition of the bracket into a sum of a Poisson one and an almost Poisson one. The corresponding rela- tion between Poisson structure and symplectic structure is proved, making use of Jacobiizer and symplecticizer. Based on analysis of pseudo-symplectic structure of constraint submanifold of Chaplygin’s nonholonomic systems, an almost Poisson bracket for the systems is constructed and decomposed into a sum of a canonical Poisson one and an almost Poisson one. Similarly, an almost Poisson structure, which can be decomposed into a sum of canonical one and an almost "Lie-Poisson" one, is also constructed on an affine space with torsion whose autoparallels are utilized to describe the free motion of some non-self-adjoint systems. The decomposition of the almost Poisson bracket di- rectly leads to a decomposition of a dynamical vector field into a sum of usual Hamiltionian vector field and an almost Hamiltonian one, which is useful to simplifying the integration of vector fields.
Brain, music, and non-Poisson renewal processes
Bianco, Simone; Ignaccolo, Massimiliano; Rider, Mark S.; Ross, Mary J.; Winsor, Phil; Grigolini, Paolo
2007-06-01
In this paper we show that both music composition and brain function, as revealed by the electroencephalogram (EEG) analysis, are renewal non-Poisson processes living in the nonergodic dominion. To reach this important conclusion we process the data with the minimum spanning tree method, so as to detect significant events, thereby building a sequence of times, which is the time series to analyze. Then we show that in both cases, EEG and music composition, these significant events are the signature of a non-Poisson renewal process. This conclusion is reached using a technique of statistical analysis recently developed by our group, the aging experiment (AE). First, we find that in both cases the distances between two consecutive events are described by nonexponential histograms, thereby proving the non-Poisson nature of these processes. The corresponding survival probabilities Ψ(t) are well fitted by stretched exponentials [ Ψ(t)∝exp (-(γt)α) , with 0.5music composition yield μmusic on the human brain.
Differential expression analysis for RNAseq using Poisson mixed models.
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.
Modeling environmental noise exceedances using non-homogeneous Poisson processes.
Guarnaccia, Claudio; Quartieri, Joseph; Barrios, Juan M; Rodrigues, Eliane R
2014-10-01
In this work a non-homogeneous Poisson model is considered to study noise exposure. The Poisson process, counting the number of times that a sound level surpasses a threshold, is used to estimate the probability that a population is exposed to high levels of noise a certain number of times in a given time interval. The rate function of the Poisson process is assumed to be of a Weibull type. The presented model is applied to community noise data from Messina, Sicily (Italy). Four sets of data are used to estimate the parameters involved in the model. After the estimation and tuning are made, a way of estimating the probability that an environmental noise threshold is exceeded a certain number of times in a given time interval is presented. This estimation can be very useful in the study of noise exposure of a population and also to predict, given the current behavior of the data, the probability of occurrence of high levels of noise in the near future. One of the most important features of the model is that it implicitly takes into account different noise sources, which need to be treated separately when using usual models.
Probability Measure of Navigation pattern predition using Poisson Distribution Analysis
Dr.V.Valli Mayil
2012-06-01
Full Text Available The World Wide Web has become one of the most important media to store, share and distribute information. The rapid expansion of the web has provided a great opportunity to study user and system behavior by exploring web access logs. Web Usage Mining is the application of data mining techniques to large web data repositories in order to extract usage patterns. Every web server keeps a log of all transactions between the server and the clients. The log data which are collected by web servers contains information about every click of user to the web documents of the site. The useful log information needs to be analyzed and interpreted in order to obtainknowledge about actual user preferences in accessing web pages. In recent years several methods have been proposed for mining web log data. This paper addresses the statistical method of Poisson distribution analysis to find out the higher probability session sequences which is then used to test the web application performance.The analysis of large volumes of click stream data demands the employment of data mining methods. Conducting data mining on logs of web servers involves the determination of frequently occurring access sequences. A statistical poisson distribution shows the frequency probability of specific events when the average probability of a single occurrence is known. The Poisson distribution is a discrete function wich is used in this paper to find out the probability frequency of particular page is visited by the user.