A fast algorithm for particle simulations
Journal of Computational Physics
Journal of Computational Chemistry
Simplifying surfaces with color and texture using quadric error metrics
Proceedings of the conference on Visualization '98
Dual contouring of hermite data
Proceedings of the 29th annual conference on Computer graphics and interactive techniques
TexMol: Interactive Visual Exploration of Large Flexible Multi-Component Molecular Complexes
VIS '04 Proceedings of the conference on Visualization '04
An algebraic spline model of molecular surfaces
Proceedings of the 2007 ACM symposium on Solid and physical modeling
Quality meshing of implicit solvation models of biomolecular structures
Computer Aided Geometric Design - Special issue: Applications of geometric modeling in the life sciences
2009 SIAM/ACM Joint Conference on Geometric and Physical Modeling
Multi-level grid algorithms for faster molecular energetics
Proceedings of the 14th ACM Symposium on Solid and Physical Modeling
SIAM Journal on Scientific Computing
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The total free energy of a molecule includes the classical molecular mechanical energy (which is understood as the free energy in vacuum) and the solvation energy, which is caused by the change of the environment of the molecule (solute) from vacuum to solvent. The solvation energy is important to the study of the intermolecular interactions. In this paper we develop a fast surface-based generalized Born method to compute the electrostatic solvation energy along with the energy derivatives for the solvation forces. The most time-consuming computation is the evaluation of the surface integrals over an algebraic spline molecular surface (ASMS), and the fast computation is achieved by the use of the nonequispaced fast Fourier transform (NFFT) algorithm. The main results of this paper involve (a) an efficient sampling of quadrature points over the molecular surface by using nonlinear patches, (b) fast linear time estimation of energy and intermolecular forces, (c) error analysis, and (d) efficient implementation combining fast pairwise summation and the continuum integration using nonlinear patches.