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Evaluation of the electrostatic properties of biomolecules has become a standard practice in molecular biophysics. Foremost among the models used to elucidate the electrostatic potential is the Poisson-Boltzmann equation; however, existing methods for solving this equation have limited the scope of accurate electrostatic calculations to relatively small(More)
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)
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)
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)
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)
that linear, mixed variational problems, and their numerical approximation by mixed finite element methods, can be studied using the powerful, abstract language of Hilbert complexes. In another recent article [arXiv:1005.4455], we extended the Arnold–Falk–Winther framework by analyzing variational crimes (a la Strang) on Hilbert complexes. In particular,(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)
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)