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Analysis of fast boundary-integral approximations for modeling electrostatic contributions of molecular binding

Amelia B. Kreienkamp, Lucy Y. Liu, Mona S. Minkara, Matthew G. Knepley, Jaydeep P. Bardhan, Mala L. Radhakrishnan (2013)

Molecular Based Mathematical Biology

We analyze and suggest improvements to a recently developed approximate continuum-electrostatic model for proteins. The model, called BIBEE/I (boundary-integral based electrostatics estimation with interpolation), was able to estimate electrostatic solvation free energies to within a mean unsigned error of 4% on a test set of more than 600 proteins¶a significant improvement over previous BIBEE models. In this work, we tested the BIBEE/I model for its capability to predict residue-by-residue interactions...

Approximation by generalized impedance boundary conditions of a transmission problem in acoustic scattering

Xavier Antoine, Hélène Barucq (2005)

ESAIM: Mathematical Modelling and Numerical Analysis - Modélisation Mathématique et Analyse Numérique

This paper addresses some results on the development of an approximate method for computing the acoustic field scattered by a three-dimensional penetrable object immersed into an incompressible fluid. The basic idea of the method consists in using on-surface differential operators that locally reproduce the interior propagation phenomenon. This approach leads to integral equation formulations with a reduced computational cost compared to standard integral formulations coupling both the transmitted...

Approximation by generalized impedance boundary conditions of a transmission problem in acoustic scattering

Xavier Antoine, Hélène Barucq (2010)

ESAIM: Mathematical Modelling and Numerical Analysis

This paper addresses some results on the development of an approximate method for computing the acoustic field scattered by a three-dimensional penetrable object immersed into an incompressible fluid. The basic idea of the method consists in using on-surface differential operators that locally reproduce the interior propagation phenomenon. This approach leads to integral equation formulations with a reduced computational cost compared to standard integral formulations coupling both the transmitted...

Approximations by the Cauchy-type integrals with piecewise linear densities

Jaroslav Drobek (2012)

Applications of Mathematics

The paper is a contribution to the complex variable boundary element method, shortly CVBEM. It is focused on Jordan regions having piecewise regular boundaries without cusps. Dini continuous densities whose modulus of continuity ω ( · ) satisfies lim sup s 0 ω ( s ) ln 1 s = 0 are considered on these boundaries. Functions satisfying the Hölder condition of order α , 0 < α 1 , belong to them. The statement that any Cauchy-type integral with such a density can be uniformly approximated by a Cauchy-type integral whose density is a piecewise...

Boundary augmented Lagrangian method for the Signorini problem

Shougui Zhang, Xiaolin Li (2016)

Applications of Mathematics

An augmented Lagrangian method, based on boundary variational formulations and fixed point method, is designed and analyzed for the Signorini problem of the Laplacian. Using the equivalence between Signorini boundary conditions and a fixed-point problem, we develop a new iterative algorithm that formulates the Signorini problem as a sequence of corresponding variational equations with the Steklov-Poincaré operator. Both theoretical results and numerical experiments show that the method presented...

Concepts—An object-oriented software package for partial differential equations

Philipp Frauenfelder, Christian Lage (2002)

ESAIM: Mathematical Modelling and Numerical Analysis - Modélisation Mathématique et Analyse Numérique

Object oriented design has proven itself as a powerful tool in the field of scientific computing. Several software packages, libraries and toolkits exist, in particular in the FEM arena that follow this design methodology providing extensible, reusable, and flexible software while staying competitive to traditionally designed point tools in terms of efficiency. However, the common approach to identify classes is to turn data structures and algorithms of traditional implementations into classes such...

Concepts—An Object-Oriented Software Package for Partial Differential Equations

Philipp Frauenfelder, Christian Lage (2010)

ESAIM: Mathematical Modelling and Numerical Analysis

Object oriented design has proven itself as a powerful tool in the field of scientific computing. Several software packages, libraries and toolkits exist, in particular in the FEM arena that follow this design methodology providing extensible, reusable, and flexible software while staying competitive to traditionally designed point tools in terms of efficiency. However, the common approach to identify classes is to turn data structures and algorithms of traditional implementations into ...

Convergence of some adaptive FEM-BEM coupling for elliptic but possibly nonlinear interface problems

Markus Aurada, Michael Feischl, Dirk Praetorius (2012)

ESAIM: Mathematical Modelling and Numerical Analysis

We consider the symmetric FEM-BEM coupling for the numerical solution of a (nonlinear) interface problem for the 2D Laplacian. We introduce some new a posteriori error estimators based on the (h − h/2)-error estimation strategy. In particular, these include the approximation error for the boundary data, which allows to work with discrete boundary integral operators only. Using the concept of estimator reduction, we prove that the proposed adaptive...

Convergence of some adaptive FEM-BEM coupling for elliptic but possibly nonlinear interface problems

Markus Aurada, Michael Feischl, Dirk Praetorius (2012)

ESAIM: Mathematical Modelling and Numerical Analysis

We consider the symmetric FEM-BEM coupling for the numerical solution of a (nonlinear) interface problem for the 2D Laplacian. We introduce some new a posteriori error estimators based on the (h − h/2)-error estimation strategy. In particular, these include the approximation error for the boundary data, which allows to work with discrete boundary integral operators only. Using the concept of estimator reduction, we prove that the proposed adaptive...

Effective semi-analytic integration for hypersingular Galerkin boundary integral equations for the Helmholtz equation in 3D

Jan Zapletal, Jiří Bouchala (2014)

Applications of Mathematics

We deal with the Galerkin discretization of the boundary integral equations corresponding to problems with the Helmholtz equation in 3D. Our main result is the semi-analytic integration for the bilinear form induced by the hypersingular operator. Such computations have already been proposed for the bilinear forms induced by the single-layer and the double-layer potential operators in the monograph The Fast Solution of Boundary Integral Equations by O. Steinbach and S. Rjasanow and we base our computations...

Efficient representations of Green’s functions for some elliptic equations with piecewise-constant coefficients

Yuri Melnikov (2010)

Open Mathematics

Convenient for immediate computer implementation equivalents of Green’s functions are obtained for boundary-contact value problems posed for two-dimensional Laplace and Klein-Gordon equations on some regions filled in with piecewise homogeneous isotropic conductive materials. Dirichlet, Neumann and Robin conditions are allowed on the outer boundary of a simply-connected region, while conditions of ideal contact are assumed on interface lines. The objective in this study is to widen the range of...

Generalized combined field integral equations for the iterative solution of the three-dimensional Helmholtz equation

Xavier Antoine, Marion Darbas (2007)

ESAIM: Mathematical Modelling and Numerical Analysis

This paper addresses the derivation of new second-kind Fredholm combined field integral equations for the Krylov iterative solution of tridimensional acoustic scattering problems by a smooth closed surface. These integral equations need the introduction of suitable tangential square-root operators to regularize the formulations. Existence and uniqueness occur for these formulations. They can be interpreted as generalizations of the well-known Brakhage-Werner [A. Brakhage and P. Werner, Arch....

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