Construction of molecular surfaces

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Table of contents

Introduction
1 The larger context
2 Implicit solvation models
3 Domain decomposition methods for implicit solvation models
I Molecular Surfaces
1 Mathematical analysis and calculation of molecular surfaces
1.1 Introduction
1.2 Introduction to implicit surfaces
1.3 Implicit molecular surfaces
1.4 Solvent accessible surface
1.5 Solvent excluded surface
1.6 Construction of molecular surfaces
1.7 Numerical results
1.8 Conclusion
2 Meshing molecular surfaces based on analytical implicit representa- tion
2.1 Introduction
2.2 Molecular surfaces
2.3 Construction of molecular surfaces
2.4 Molecular inner holes
2.5 Meshing
2.6 Conclusion
II Domain Decomposition Method for Implicit Solvation Models
3 Domain Decomposition Method for the Polarizable Continuum Model based on the Solvent Excluded Surface
3.1 Introduction
3.2 Solute-solvent boundary
3.3 Dielectric permittivity function
3.4 Problem formulation and global strategy
3.5 Domain decomposition strategy
3.6 Single-domain solvers
3.7 Numerical results
3.8 Conclusion
4 Domain Decomposition Method for the Poisson-Boltzmann Solvation Model
4.1 Introduction
4.2 PB solvation model
4.3 Problem transformation
4.4 Strategy
4.5 Single-domain solvers
4.6 Global linear system
4.7 Numerical results
4.8 Conclusion
Appendices
A Proof of Theorem 1.5.1
B Advancing-front algorithm for a spherical patch
C Appendices in Chapter 3
C.1 Well-posedness of (3.6.7)
C.2 Computation of @ @Y m ℓ and @ @φY m ℓ
C.3 Computation of f(x) in (3.6.6)
D Computation of C1; C2; F0 173
Bibliography