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- Ivar Stakgold, Michael Holst
- 2010

No part of this publication may be reproduced, stored in a retrieval system, or transmitted in any form or by any means Limit of Liability/Disclaimer of Warranty: While the publisher and author have used their best efforts in preparing this book, they make no representations or warranties with respect to the accuracy or completeness of the contents of this… (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)

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)

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)

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)

- M. J. Holst, Michael J. Holst
- 1994

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)

- Benzhuo Lu, Y C Zhou, Gary A Huber, Stephen D Bond, Michael J Holst, J Andrew McCammon
- The Journal of chemical physics
- 2007

A computational framework is presented for the continuum modeling of cellular biomolecular diffusion influenced by electrostatic driving forces. This framework is developed from a combination of state-of-the-art numerical methods, geometric meshing, and computer visualization tools. In particular, a hybrid of (adaptive) finite element and boundary element… (More)