A multigrid method is presented for the numerical solution of the linearized Poisson-Boltzmann equation arising in molecular biophysics. The equation is discretized with the finite volume method, and the numerical solution of the discrete equations is accomplished with multiple grid techniques originally developed for two-dimensional interface problems occurring in reactor physics. A detailed analysis of the resulting method is presented for several computer architectures, including comparisons to diagonally scaled CG, ICCG, vectorized ICCG and MICCG, and to SOR provided with an optimal relaxation parameter. Our results indicate that the multigrid method is superior to the preconditioned CG methods and SOR, and that the advantage of multigrid grows with the problem size.

We present a robust and efficient numerical method for solution of the nonlinear Poisson-Boltzmann equation arising in molecular biophysics. The equation is discretized with the box method, and solution of the discrete equations is accomplished with a global inexact-Newton method, combined with linear multilevel techniques we have described in a paper appearing previously in this journal. A detailed analysis of the resulting method is presented, with comparisons to other methods that have been proposed in the literature, including the classical nonlinear multigrid method, the nonlinear conjugate gradient method, and nonlinear relaxation methods such as successive over-relaxation. Both theoretical and numerical evidence suggests that this method will converge in the case of molecules for which many of the existing methods will not. In addition, for problems which the other methods are able to solve, numerical experiments show that the new method is substantially more efficient, and the superiority of this method grows with the problem size. The method is easy to implement once a linear multilevel solver is available, and can also easily be used in conjunction with linear methods other than multigrid.

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The nonlinear Poisson-Boltzmann equation (NPBE) provides a continuum description of the electrostatic field in an ionic medium around a macromolecule. Here, a novel approach to the solution of the full NPBE is developed. This robust and efficient algorithm combines multilevel techniques with a damped inexact Newton's method. The CPU time required for solution of the full NPBE, which is less than that for standard single-grid approaches in solving the corresponding linearized equation, is proportional to the number of unknowns enabling applications to very large macromolecular systems. Convergence of the method is demonstrated for a variety of protein systems. Comparison of the solutions to the linearized Poisson-Boltzmann equation shows that the damping of the electrostatic field around the charge is increased and that the potential scales logarithmically with charge. The inclusion of the full nonlinearity thus reduces the impact of highly charged residues on protein surfaces and provides a more realistic representation of electrostatic effects. This is demonstrated through calculation of potential around the active site regions of the 1,266-residue tryptophan synthase dimer and in the computation of rate constants from Brownian dynamics calculations in the superoxide dismutase-superoxide and antibody-antigen systems.

Binary black hole interactions provide potentially the strongest source of gravitational radiation for detectors currently under development. We present some results from the Binary Black Hole Grand Challenge Alliance three-dimensional Cauchy evolution module. These constitute essential steps towards modeling such interactions and predicting gravitational radiation waveforms. We report on single black hole evolutions and the first successful demonstration of a black hole moving freely through a three-dimensional computational grid via a Cauchy evolution: a hole moving ∼ 6M at 0.1c during a total evolution of duration ∼ 60M . The accurate computational modeling of black-hole interactions is essential to the confident detection of astrophysical gravitational radiation by future space-based detectors such as LISA and by the LIGO/VIRGO/GEO complex of ground-based detectors currently under construction. The sensitivity of these detectors will be significantly enhanced if accurate computer simulations of black-hole mergers can produce predictions of radiation waveforms [1]. The Binary Black Hole Grand Challenge Alliance [2] was funded in September 1993 to develop the computational infrastructure necessary accurately to simulate the coalescence of black-hole binaries. The primary objective of the resulting code will be the production of waveforms from binary black hole mergers. In this Letter we report on an important step towards achieving such simulations.A key difficulty in evolving black-hole spacetimes is handling the curvature singularity contained within each hole. The only viable means of accomplishing this over time scales required for binary coalescence appears to be black-hole excision: exclude all or part of the black-hole interior (and the singularity) from the computational domain and evolve only the exterior region [3,4

We present a method for extracting gravitational radiation from a three-dimensional numerical relativity simulation and, using the extracted data, to provide outer boundary conditions. The method treats dynamical gravitational variables as nonspherical perturbations of Schwarzschild geometry. We discuss a code which implements this method and present results of tests which have been performed with a three-dimensional numerical relativity code. [S0031-9007(98)05380-0] PACS numbers: 04.25. Dm, 04.30.Db, 04.70.Bw Numerical relativity represents the only currently viable method for obtaining solutions to Einstein equations for highly dynamical and strong field sources of gravitational radiation. Using these techniques to study coalescing black hole binaries is the purpose of the multi-institutional Binary Black Hole "Grand Challenge" Alliance effort [1] which is presently underway in the United States. This effort is also motivated by the prospect of observations with the next generation of gravitational wave detectors.In addition to tremendous demands on computational resources, implementing the standard 3 1 1 [2,3] formulation of Einstein theory as a Cauchy problem [4] is complicated considerably by the necessity of imposing boundary conditions which maintain numerical accuracy and the physical correctness of the solution. Both inner and outer boundary conditions have received considerable attention. Recent efforts on interior boundaries have focused on the excision of the interior of the black hole from the computational domain (see, for example, [5]). This paper will concentrate on the problem of outer boundary conditions applied at a finite radius around a source of gravitational waves.Proper boundary conditions on spacelike slices of asymptotically flat spacetimes are essential for the accurate computation of the gravitational wave forms produced in the strong field region that represent the observationally relevant aspect of the computation. Since it is not feasible to simulate on spacelike slices out to arbitrarily large distances from the source, it is necessary to extract gravitational waves comparatively near the strong field region and to have boundary conditions that allow radiation to pass cleanly off the mesh. If poor outgoing boundary conditions are imposed, spurious radiation is produced which can contaminate the computed gravitational wave form. Additionally, the outer boundary is usually close enough to the isolated source that backscatter of radiation from curvature is significant. This source of incoming radiation needs to be built into the outer boundary conditions. An approach to the extraction of gravitational wave information and the computation of outer boundary conditions that exploits the matching of the interior numerical solution with an exterior perturbative solution on spacelike slices has been developed during the past decade and applied to a number of different physical scenarios [6][7][8]. Extension of these techniques to three-dimensional (3D) simulations has been one of the ef...

We report new results which establish that the accurate three-dimensional numerical simulation of generic single-black-hole spacetimes has been achieved by characteristic evolution with unlimited long term stability. Our results include distorted, moving, and spinning single black holes, with evolution times up to 60 000M. [S0031-9007(98)

A realistic 40 nm InAs high electron mobility transistor is studied using a two-dimensional, full-band, and atomistic Schrödinger-Poisson solver based on the sp 3 d 5 s * tightbinding model. Bandstructure non-parabolicity effects, strain, alloy disorder in the InGaAs and InAlAs barriers, as well as band-to-band tunneling in the transistor OFF-state are automatically included through the full-band atomistic model. The source and drain contact extensions are taken into account a posteriori by adding two series resistances to the device channel. The simulated current characteristics are compared to measured data and show a good quantitative agreement.