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The convergence and optimality of adaptive mixed finite element methods for the Poisson equation are established in this paper. The main difficulty for mixed finite element methods is the lack of minimization principle and thus the failure of orthogonal-ity. A quasi-orthogonality property is proved using the fact that the error is orthogonal to the(More)
We present a new approach to the use of parallel computers with adaptive finite element methods. This approach addresses the load balancing problem in a new way, requiring far less communication than current approaches. It also allows existing sequential adaptive PDE codes such as PLTMG and MC to run in a parallel environment without a large investment in(More)
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(More)
A widely used electrostatics model in the biomolecular modeling community , the nonlinear Poisson–Boltzmann equation, along with its finite element approximation , are analyzed in this paper. A regularized Poisson–Boltzmann equation is introduced as an auxiliary problem, making it possible to study the original nonlinear equation with delta distribution(More)
Adaptive multilevel finite element methods are developed and analyzed for certain elliptic systems arising in geometric analysis and general relativity. This class of nonlinear elliptic systems of tensor equations on mani-folds is first reviewed, and then adaptive multilevel finite element methods for approximating solutions to this class of problems are(More)
We apply the adaptive multilevel finite element techniques described in [20] to the nonlinear Poisson-Boltzmann equation (PBE) in the context of biomolecules. Fast and accurate numerical solution of the PBE in this setting is usually difficult to accomplish due to presence of discontinuous coefficients, delta functions, three spatial dimensions, unbounded(More)
1 Superconvergent discontinuous Galerkin methods for second-order elliptic problems / A multiscale finite element method for partial differential equations posed in domains with rough boundaries / Alexandre L. Madureira 35 Convergence and optimality of adaptive mixed finite element methods / 79 Overlapping additive Schwarz preconditioners for elliptic PDEs(More)
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(More)
Using new methods for the parallel solution of elliptic partial differential equations, the teraflops computing power of massively parallel computers can be leveraged to perform electrostatic calculations on large biological systems. This paper describes the adaptive multilevel finite element solution of the Poisson-Boltzmann equation for a microtubule on(More)