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We present a multigrid algorithm for self consistent solution of the Kohn-Sham equations in real space. The entire problem is discretized on a real space mesh with a high order finite difference representation. The resulting self consistent equations are solved on a heirarchy of grids of increasing resolution with a nonlinear Full Approximation Scheme, Full(More)
ClC chloride channels possess a homodimeric structure in which each monomer contains an independent chloride ion pathway. ClC channel gating is regulated by chloride ion concentration, pH, and voltage. Based on structural and physiological evidence, it has been proposed that a glutamate residue on the extracellular end of the selectivity filter acts as a(More)
Iterative multiscale methods for electronic structure calculations offer several advantages for large-scale problems. Here we examine a nonlinear full approximation scheme (FAS) multigrid method for solving fixed potential and self-consistent eigenvalue problems. In principle, the expensive orthogonalization and Ritz projection operations can be moved to(More)
The finely tuned structures of membrane channel proteins allow selective passage of ions through the available aqueous pores. To understand channel function, it is crucial to locate the pores and study their physical and chemical properties. Here, we propose a new pore-searching algorithm (TransPath), which uses the Configurational Bias Monte Carlo (CBMC)(More)
ClC chloride channels possess a homodimeric structure in which each monomer contains an independent chloride ion pathway. ClC channel gating is regulated by chloride ion concentration, pH and voltage. Based on structural and physiological evidence, it has been proposed that a glutamate residue on the extracellular end of the selectivity filter acts as a(More)
A new method for performing high order mesh reenement multigrid computations in real space is presented. The method allows for accurate linear scaling electrostatics calculations over composite domains with local nested ne patches. The Full Approximation Scheme (FAS) multigrid technique is utilized for a sequence of reenement patches of increasing(More)
A method for performing high order mesh refinement multigrid computations is presented. The Full Approximation Scheme (FAS) multigrid technique is utilized for a sequence of nested patches of increasing resolution. Conservation forms are generated on coarse scales by additional defect correction terms which counter the local excess fluxes at the boundaries.(More)
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