A fast algorithm for particle simulations
Journal of Computational Physics
An analysis of quadrature errors in second-kind boundary integral methods
SIAM Journal on Numerical Analysis
Journal of Computational Chemistry
Journal of Computational Chemistry
Journal of Computational Chemistry
The electric potential of a macromolecule in a solvent: A fundamental approach
Journal of Computational Physics
Numerical quadratures for layer potentials over curved domains in R3
SIAM Journal on Numerical Analysis
Multigrid solution of the Poisson-Boltzmann equation
Journal of Computational Chemistry
Multilevel methods for the Poisson-Boltzmann equation
Multilevel methods for the Poisson-Boltzmann equation
Boundary value problems of mathematical physics (vol. 2)
Boundary value problems of mathematical physics (vol. 2)
A Generalization of Algebraic Surface Drawing
ACM Transactions on Graphics (TOG)
Computer-Aided Drug Design: Methods and Applications
Computer-Aided Drug Design: Methods and Applications
Smooth Shell Construction with Mixed Prism Fat Surfaces
Geometric Modelling
Fast methods for simulation of biomolecule electrostatics
Proceedings of the 2002 IEEE/ACM international conference on Computer-aided design
A kernel-independent adaptive fast multipole algorithm in two and three dimensions
Journal of Computational Physics
TexMol: Interactive Visual Exploration of Large Flexible Multi-Component Molecular Complexes
VIS '04 Proceedings of the conference on Visualization '04
A New Parallel Kernel-Independent Fast Multipole Method
Proceedings of the 2003 ACM/IEEE conference on Supercomputing
An algebraic spline model of molecular surfaces
Proceedings of the 2007 ACM symposium on Solid and physical modeling
A high-order 3D boundary integral equation solver for elliptic PDEs in smooth domains
Journal of Computational Physics
The Finite Element Approximation of the Nonlinear Poisson-Boltzmann Equation
SIAM Journal on Numerical Analysis
Higher-order level-set method and its application in biomolecular surfaces construction
Journal of Computer Science and Technology
Quality meshing of implicit solvation models of biomolecular structures
Computer Aided Geometric Design - Special issue: Applications of geometric modeling in the life sciences
$F^2$Dock: Fast Fourier Protein-Protein Docking
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Fast Molecular Solvation Energetics and Forces Computation
SIAM Journal on Scientific Computing
An Algebraic Spline Model of Molecular Surfaces for Energetic Computations
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Journal of Computational Physics
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In order to compute polarization energy of biomolecules, we describe a boundary element approach to solving the linearized Poisson-Boltzmann equation. Our approach combines several important features, including the derivative boundary formulation of the problem and a smooth approximation of the molecular surface based on the algebraic spline molecular surface. State of the art software for numerical linear algebra and the kernel independent fast multipole method is used for both simplicity and efficiency of our implementation. We perform a variety of computational experiments, testing our method on a number of actual proteins involved in molecular docking and demonstrating the effectiveness of our solver for computing molecular polarization energy.