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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...

Computation of the fundamental solution of electrodynamics for anisotropic materials

Valery Yakhno, Handan Yaslan, Tatiana Yakhno (2012)

Open Mathematics

A new method for computation of the fundamental solution of electrodynamics for general anisotropic nondispersive materials is suggested. It consists of several steps: equations for each column of the fundamental matrix are reduced to a symmetric hyperbolic system; using the Fourier transform with respect to space variables and matrix transformations, formulae for Fourier images of the fundamental matrix columns are obtained; finally, the fundamental solution is computed by the inverse Fourier transform....

Convex shape optimization for the least biharmonic Steklov eigenvalue

Pedro Ricardo Simão Antunes, Filippo Gazzola (2013)

ESAIM: Control, Optimisation and Calculus of Variations

The least Steklov eigenvalue d1 for the biharmonic operator in bounded domains gives a bound for the positivity preserving property for the hinged plate problem, appears as a norm of a suitable trace operator, and gives the optimal constant to estimate the L2-norm of harmonic functions. These applications suggest to address the problem of minimizing d1 in suitable classes of domains. We survey the existing results and conjectures about this topic; in particular, the existence of a convex domain...

Method of fundamental solutions for biharmonic equation based on Almansi-type decomposition

Koya Sakakibara (2017)

Applications of Mathematics

The aim of this paper is to analyze mathematically the method of fundamental solutions applied to the biharmonic problem. The key idea is to use Almansi-type decomposition of biharmonic functions, which enables us to represent the biharmonic function in terms of two harmonic functions. Based on this decomposition, we prove that an approximate solution exists uniquely and that the approximation error decays exponentially with respect to the number of the singular points. We finally present results...

Operational Methods in the Environment of a Computer Algebra System

Spiridonova, Margarita (2009)

Serdica Journal of Computing

This article presents the principal results of the doctoral thesis “Direct Operational Methods in the Environment of a Computer Algebra System” by Margarita Spiridonova (Institute of mathematics and Informatics, BAS), successfully defended before the Specialised Academic Council for Informatics and Mathematical Modelling on 23 March, 2009.The presented research is related to the operational calculus approach and its representative applications. Operational methods are considered, as well as their...

Some variants of the method of fundamental solutions: regularization using radial and nearly radial basis functions

Csaba Gáspár (2013)

Open Mathematics

The method of fundamental solutions and some versions applied to mixed boundary value problems are considered. Several strategies are outlined to avoid the problems due to the singularity of the fundamental solutions: the use of higher order fundamental solutions, and the use of nearly fundamental solutions and special fundamental solutions concentrated on lines instead of points. The errors of the approximations as well as the problem of ill-conditioned matrices are illustrated via numerical examples....

Sweeping preconditioners for elastic wave propagation with spectral element methods

Paul Tsuji, Jack Poulson, Björn Engquist, Lexing Ying (2014)

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

We present a parallel preconditioning method for the iterative solution of the time-harmonic elastic wave equation which makes use of higher-order spectral elements to reduce pollution error. In particular, the method leverages perfectly matched layer boundary conditions to efficiently approximate the Schur complement matrices of a block LDLT factorization. Both sequential and parallel versions of the algorithm are discussed and results for large-scale problems from exploration geophysics are presented....

Total overlapping Schwarz' preconditioners for elliptic problems

Faker Ben Belgacem, Nabil Gmati, Faten Jelassi (2011)

ESAIM: Mathematical Modelling and Numerical Analysis

A variant of the Total Overlapping Schwarz (TOS) method has been introduced in [Ben Belgacem et al., C. R. Acad. Sci., Sér. 1 Math.336 (2003) 277–282] as an iterative algorithm to approximate the absorbing boundary condition, in unbounded domains. That same method turns to be an efficient tool to make numerical zooms in regions of a particular interest. The TOS method enjoys, then, the ability to compute small structures one wants to capture and the reliability to obtain the...

Total overlapping Schwarz' preconditioners for elliptic problems

Faker Ben Belgacem, Nabil Gmati, Faten Jelassi (2011)

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

A variant of the Total Overlapping Schwarz (TOS) method has been introduced in [Ben Belgacem et al., C. R. Acad. Sci., Sér. 1 Math. 336 (2003) 277–282] as an iterative algorithm to approximate the absorbing boundary condition, in unbounded domains. That same method turns to be an efficient tool to make numerical zooms in regions of a particular interest. The TOS method enjoys, then, the ability to compute small structures one wants to capture and the reliability to obtain the behavior of the solution...

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