New High-Resolution Semi-discrete Central Schemes for Hamilton–Jacobi Equations

We introduce a new high-resolution central scheme for multidimensional Hamilton–Jacobi equations. The scheme retains the simplicity of the non-oscillatory central schemes developed by C.-T. Lin and E. Tadmor (in press, SIAM J. Sci. Comput.), yet it enjoys a smaller amount of numerical viscosity, independent of 1/Δt. By letting Δt↓0 we obtain a new second-order central scheme in the particularly simple semi-discrete form, along the lines of the new semi-discrete central schemes recently introduced by the authors in the context of hyperbolic conservation laws. Fully discrete versions are obtained with appropriate Runge–Kutta solvers. The smaller amount of dissipation enables efficient integration of convection-diffusion equations, where the accumulated error is independent of a small time step dictated by the CFL limitation. The scheme is non-oscillatory thanks to the use of nonlinear limiters. Here we advocate the use of such limiters on second discrete derivatives, which is shown to yield an improved high resolution when compared to the usual limitation of first derivatives. Numerical experiments demonstrate the remarkable resolution obtained by the proposed new central scheme.     

On Backtracking Failure in Newton–GMRES Methods with a Demonstration for the Navier–Stokes Equations

In an earlier study of inexact Newton methods, we pointed out that certain counterintuitive behavior may occur when applying residual backtracking to the Navier–Stokes equations with heat and mass transport. Specifically, it was observed that a Newton–GMRES method globalized by backtracking (linesearch, damping) may be less robust when high accuracy is required of each linear solve in the Newton sequence than when less accuracy is required. In this brief discussion, we offer a possible explanation for this phenomenon, together with an illustrative numerical experiment involving the Navier–Stokes equations.     

A New Unconditionally Stable Algorithm for Steady-State Fluid Simulation of High Density Plasma Discharge

A new unconditionally stable algorithm for steady-state fluid simulation of high density plasma discharge is suggested. The physical origin of restriction on simulation time step is discussed and a new method to overcome it is explained. To compare the new method with previous other methods, a one-dimensional fluid simulation of inductively coupled plasma discharge is performed.     

A Residual-Based Compact Scheme for the Compressible Navier–Stokes Equations

A simple and efficient time-dependent method is presented for solving the steady compressible Euler and Navier–Stokes equations with third-order accuracy. Owing to its residual-based structure, the numerical scheme is compact without requiring any linear algebra, and it uses a simple numerical dissipation built on the residual. The method contains no tuning parameter. Accuracy and efficiency are demonstrated for 2-D inviscid and viscous model problems. Navier–Stokes calculations are presented for a shock/boundary layer interaction, a separated laminar flow, and a transonic turbulent flow over an airfoil.     

Comparison of Several Spatial Discretizations for the Navier–Stokes Equations

Grid convergence studies for subsonic and transonic flows over airfoils are presented in order to compare the accuracy of several spatial discretizations for the compressible Navier–Stokes equations. The discretizations include the following schemes for the inviscid fluxes: (1) second-order-accurate centered differences with third-order matrix numerical dissipation, (2) the second-order convective upstream split pressure scheme (CUSP), (3) third-order upwind-biased differencing with Roe's flux-difference splitting, and (4) fourth-order centered differences with third-order matrix numerical dissipation. The first three are combined with second-order differencing for the grid metrics and viscous terms. The fourth discretization uses fourth-order differencing for the grid metrics and viscous terms, as well as higher-order approximations near boundaries and for the numerical integration used to calculate forces and moments. The results indicate that the discretization using higher-order approximations for all terms is substantially more accurate than the others, producing less than two percent numerical error in lift and drag components on grids with less than 13,000 nodes for subsonic cases and less than 18,000 nodes for transonic cases. Since the cost per grid node of all of the discretizations studied is comparable, the higher-order discretization produces solutions of a given accuracy much more efficiently than the others.     

Multigrid Solution of the Incompressible Navier–Stokes Equations for Density-Stratified Flow past Three-Dimensional Obstacles

The steady incompressible Navier–Stokes equations in three dimensions are solved for neutral and stably stratified flow past three-dimensional obstacles of increasing spanwise width. The continuous equations are approximated using a finite volume discretisation on staggered grids with a flux-limited monotonic scheme for the advective terms. The discrete equations which arise are solved using a nonlinear multigrid algorithm with up to four grid levels using the SIMPLE pressure correction method as smoother. When at its most effective the multigrid algorithm is demonstrated to yield convergence rates which are independent of the grid density. However, it is found that the asymptotic convergence rate depends on the choice of the limiter used for the advective terms of the density equation, and some commonly used schemes are investigated. The variation with obstacle width of the influence of the stratification on the flow field is described and the results of the three-dimensional computations are compared with those of the corresponding computation of flow over a two-dimensional obstacle (of effectively infinite width). Also given are the results of time-dependent computations for three-dimensional flows under conditions of strong static stability when lee-wave propagation is present and the multigrid algorithm is used to compute the flow at each time step.     

Nonlinear Landau Damping in Spherically Symmetric Vlasov Poisson Systems

The Vlasov Poisson system is a partial differential equation widely used to describe collisionless plasma. It is formulated in a six-dimensional phase space, this prohibits a numerical solution on a complete phase space grid. In some applications, however, spherical symmetry is given, which introduces singularities into the Vlasov Poisson equation. We focus on such problems and propose a stable algorithm using accommodating boundaries. At first, the method is tested in the linear regime, where analytical solutions are available. Thereafter it is applied to large disturbances from equilibrium.     

The Three Dimensional Non-conforming Finite Element Solution of the Chapman–Ferraro Problem

We demonstrate the feasibility of using a non-conforming, piecewise harmonic finite element method on an unstructured grid in solving a magnetospheric physics problem. We use this approach to construct a global discrete model of the magnetic field of the magnetosphere that includes the effects of shielding currents at the outer boundary (the magnetopause). As in the approach of F. R. Toffolettoet al.(1994,Geophys. Res. Lett.21, 7) the internal magnetospheric field model is that of R. V. Hilmer and G.-H. Voigt (1995,J. Geophys. Res.) while the magnetopause shape is based on an empirically determined approximation (1997, J. Shueet al.,J. Geophys. Res.102, 9497). The results is a magnetic field model whose field lines are completely confined within the magnetosphere. The presented numerical results indicate that the discrete non-conforming finite element model is well-suited for magnetospheric field modeling.     

A Roe Scheme for Ideal MHD Equations on 2D Adaptively Refined Triangular Grids

In this paper we present a second order finite volume method for the resolution of the bidimensional ideal MHD equations on adaptively refined triangular meshes. Our numerical flux function is based on a multidimensional extension of the Roe scheme proposed by Cargo and Gallice for the 1D MHD system. If the mesh is only composed of triangles, our scheme is proved to be weakly consistent with the condition …B=0. This property fails on a cartesian grid. The efficiency of our refinement procedure is shown on 2D MHD shock capturing simulations. Numerical results are compared in case of the interaction of a supersonic plasma with a cylinder on the adapted grid and several non-refined grids. We also present a mass loading simulation which corresponds to a 2D version of the interaction between the solar wind and a comet.     

Modeling Three-Dimensional Multiphase Flow Using a Level Contour Reconstruction Method for Front Tracking without Connectivity

Three-dimensional multiphase flow and flow with phase change are simulated using a simplified method of tracking and reconstructing the phase interface. The new level contour reconstruction technique presented here enables front tracking methods to naturally, automatically, and robustly model the merging and breakup of interfaces in three-dimensional flows. The method is designed so that the phase surface is treated as a collection of physically linked but not logically connected surface elements. Eliminating the need to bookkeep logical connections between neighboring surface elements greatly simplifies the Lagrangian tracking of interfaces, particularly for 3D flows exhibiting topology change. The motivation for this new method is the modeling of complex three-dimensional boiling flows where repeated merging and breakup are inherent features of the interface dynamics. Results of 3D film boiling simulations with multiple interacting bubbles are presented. The capabilities of the new interface reconstruction method are also tested in a variety of two-phase flows without phase change. Three-dimensional simulations of bubble merging and droplet collision, coalescence, and breakup demonstrate the new method's ability to easily handle topology change by film rupture or filamentary breakup. Validation tests are conducted for drop oscillation and bubble rise. The susceptibility of the numerical method to parasitic currents is also thoroughly assessed.     

Positive Numerical Integration Methods for Chemical Kinetic Systems

Chemical kinetics conserves mass and renders nonnegative solutions; a good numerical simulation would ideally produce mass-balanced, positive concentration vectors. Many time-stepping methods are mass conservative; however, unconditional positivity restricts the order of a traditional method to one. The projection method presented in this paper ensures mass conservation and positivity. First, a numerical approximation is computed with one step of a mass-preserving traditional scheme. If there are negative components, the nearest vector in the reaction simplex is found by solving a quadratic optimization problem; this vector is shown to better approximate the true solution. A simpler version involves just one projection step and stabilizes the reaction simplex. This technique works best when the underlying time-stepping scheme favors positivity. Projected methods are more accurate than clipping and allow larger time steps for kinetic systems which are unstable outside the positive quadrant.     

Transparent Boundary Conditions for Split-Step Padé Approximations of the One-Way Helmholtz Equation

In this paper, we generalize the nonlocal discrete transparent boundary condition introduced by F. Schmidt and P. Deuflhard (1995, Comput. Math. Appl.29, 53–76) and by F. Schmidt and D. Yevick (1997, J. Comput. Phys.134, 96–107) to propagation methods based on arbitrary Padé approximations of the two-dimensional one-way Helmholtz equation. Our approach leads to a recursive formula for the coefficients appearing in the nonlocal condition, which then yields an unconditionally stable propagation method.     

An Efficient NMR Experiment for Analyzing Sugar-Puckering in Unlabeled DNA: Application to the 26-kDa Dead Ringer–DNA Complex

We present a new NMR experiment for estimating the type and degree of sugar-puckering in high-molecular-weight unlabeled DNA molecules. The experiment consists of a NOESY sequence preceded by a constant-time scalar coupling period. Two subexperiments are compared, each differing in the amount of time the (3)J(H3'H2') and (3)J(H3'H2") couplings are active on the H3' magnetization. The resultant data are easy to analyze, since a comparison of the signal intensities of any resolved NOE cross peak originating from H3' atoms of the duplex can be used to estimate the sum of the (3)J(H3'H2') and (3)J(H3'H2") couplings and thus the puckering type of the deoxyribose ring. Isotope filters to eliminate signals of the (13)C-labeled component in the F1-dimension are implemented, facilitating analyses of high-molecular-weight protein-DNA complexes containing (13)C-labeled protein and unlabeled DNA. The utility of the experiment is demonstrated on the 26-kDa Dead Ringer protein-DNA complex and reveals that the DNA uniformly adopts the S-type configuration when bound to protein.     

Physics-Based Preconditioning and the Newton–Krylov Method for Non-equilibrium Radiation Diffusion

An algorithm is presented for the solution of the time dependent reaction-diffusion systems which arise in non-equilibrium radiation diffusion applications. This system of nonlinear equations is solved by coupling three numerical methods, Jacobian-free Newton–Krylov, operator splitting, and multigrid linear solvers. An inexact Newton's method is used to solve the system of nonlinear equations. Since building the Jacobian matrix for problems of interest can be challenging, we employ a Jacobian–free implementation of Newton's method, where the action of the Jacobian matrix on a vector is approximated by a first order Taylor series expansion. Preconditioned generalized minimal residual (PGMRES) is the Krylov method used to solve the linear systems that come from the iterations of Newton's method. The preconditioner in this solution method is constructed using a physics-based divide and conquer approach, often referred to as operator splitting. This solution procedure inverts the scalar elliptic systems that make up the preconditioner using simple multigrid methods. The preconditioner also addresses the strong coupling between equations with local 2×2 block solves. The intra-cell coupling is applied after the inter-cell coupling has already been addressed by the elliptic solves. Results are presented using this solution procedure that demonstrate its efficiency while incurring minimal memory requirements.     

MUSIC and Aromatic Residues: Amino Acid Type-Selective H–N Correlations, III

Amino acid type-selective experiments can help to remove ambiguities in automated assignment procedures for ¹⁵N/¹³C-labeled proteins. Here we present five triple-resonance experiments that yield amino acid type-selective ¹H–¹⁵N correlations for aromatic amino acids. Four of the novel experiments are based on the MUSIC coherence transfer scheme that replaces the initial INEPT transfer and is selective for CH₂. The MUSIC sequence is combined with selective excitation pulses to create experiments for Trp (W-HSQC) as well as Phe, Tyr, and His (FYH-HSQC). In addition, an experiment selective for Trp H¹–N¹ is presented. The new experiments are recorded as two-dimensional experiments and their performance is demonstrated with the application to a protein domain of 115 amino acids.     

Approximation and Reconstruction of the Electrostatic Field in Wire–Plate Precipitators by a Low-Order Model

The numerical computation of the ionic space charge and electric field produced by corona discharge in a wire–plate electrostatic precipitator (ESP) is considered. The electrostatic problem is defined by a reduced set of the Maxwell equations. Since self-consistent conditions at the wire and at the plate cannot be specified a priori, a time-consuming iterative numerical procedure is required. The efficiency of all numerical solvers of the reduced Maxwell equations depends in particular on the accuracy of the initial guess solution. The objectives of this work are two: first, we propose a semianalytical technique based on the Karhunen–Loève (KL) decomposition of the current density field J, which can significantly improve the performance of a numerical solver; second, we devise a procedure to reconstruct the complete electric field from a given J. The approximate solution of the current density field is based on the derivation of an analytical approximation , which, added to a linear combination of few KL basis functions, constitutes an accurate approximation of J. In the first place, this result is useful for optimization procedures of the current density field, which involve the computation of many different configurations. Second, we show that from the current density field we can obtain an accurate estimate for the complete electrostatic field which can be used to speed up the convergence of the iterative procedure of standard numerical solvers.     

A General-Purpose Finite-Volume Advection Scheme for Continuous and Discontinuous Fields on Unstructured Grids

We present a new general-purpose advection scheme for unstructured meshes based on the use of a variation of the interface-tracking flux formulation recently put forward by O. Ubbink and R. I. Issa (J. Comput. Phys.153, 26 (1999)), in combination with an extended version of the flux-limited advection scheme of J. Thuburn (J. Comput. Phys.123, 74 (1996)), for continuous fields. Thus, along with a high-order mode for continuous fields, the new scheme presented here includes optional integrated interface-tracking modes for discontinuous fields. In all modes, the method is conservative, monotonic, and compatible. It is also highly shape preserving. The scheme works on unstructured meshes composed of any kind of connectivity element, including triangular and quadrilateral elements in two dimensions and tetrahedral and hexahedral elements in three dimensions. The scheme is finite-volume based and is applicable to control-volume finite-element and edge-based node-centered computations. An explicit–implicit extension to the continuous-field scheme is provided only to allow for computations in which the local Courant number exceeds unity. The transition from the explicit mode to the implicit mode is performed locally and in a continuous fashion, providing a smooth hybrid explicit–implicit calculation. Results for a variety of test problems utilizing the continuous and discontinuous advection schemes are presented.     

A New Version of the Fast Multipole Method for Screened Coulomb Interactions in Three Dimensions

We present a new version of the fast multipole method (FMM) for screened Coulomb interactions in three dimensions. Existing schemes can compute such interactions in O(N) time, where N denotes the number of particles. The constant implicit in the O(N) notation, however, is dominated by the expense of translating far-field spherical harmonic expansions to local ones. For each box in the FMM data structure, this requires 189p⁴ operations per box, where p is the order of the expansions used. The new formulation relies on an expansion in evanescent plane waves, with which the amount of work can be reduced to 40p²+6p³ operations per box.     

A Finite Volume Method for the Approximation of Diffusion Operators on Distorted Meshes

A new finite volume method is presented for discretizing general linear or nonlinear elliptic second-order partial-differential equations with mixed boundary conditions. The advantage of this method is that arbitrary distorted meshes can be used without the numerical results being altered. The resulting algorithm has more unknowns than standard methods like finite difference or finite element methods. However, the matrices that need to be inverted are positive definite, so the most powerful linear solvers can be applied. The method has been tested on a few elliptic and parabolic equations, either linear, as in the case of the standard heat diffusion equation, or nonlinear, as in the case of the radiation diffusion equation and the resistive diffusion equation with Hall term.     

The Numerical Methods for Oscillating Singularities in Elliptic Boundary Value Problems

The singularities near the crack tips of homogeneous materials are monotone of type r^α and r^α log^δr (depending on the boundary conditions along nonsmooth domains). However, the singularities around the interfacial cracks of the heterogeneous bimaterials are oscillatory of type r^α sin( log r). The method of auxiliary mapping (MAM), introduced by Babu ka and Oh, was proven to be successful in dealing with r^α type singularities. However, the effectiveness of MAM is reduced in handling oscillating singularities. This paper deals with oscillating singularities as well as the monotone singularities by extending MAM through introducing the power auxiliary mapping and the exponential auxiliary mapping.