Marching cubes: A high resolution 3D surface construction algorithm
SIGGRAPH '87 Proceedings of the 14th annual conference on Computer graphics and interactive techniques
A real-time malleable molecular surface
Journal of Molecular Graphics
Area and volume coherence for efficient visualization of 3D scalar functions
VVS '90 Proceedings of the 1990 workshop on Volume visualization
Symbolic local refinement of tetrahedral grids
Journal of Symbolic Computation
Multilevel methods for the Poisson-Boltzmann equation
Multilevel methods for the Poisson-Boltzmann equation
Local bisection refinement for N-simplicial grids generated by reflection
SIAM Journal on Scientific Computing
Triangulating the surface of a molecule
Discrete Applied Mathematics - Special volume on computational molecular biology
Multiresolution tetrahedral framework for visualizing regular volume data
VIS '97 Proceedings of the 8th conference on Visualization '97
Using distance maps for accurate surface representation in sampled volumes
VVS '98 Proceedings of the 1998 IEEE symposium on Volume visualization
Time critical isosurface refinement and smoothing
VVS '00 Proceedings of the 2000 IEEE symposium on Volume visualization
Proceedings of the conference on Visualization '00
Interactive view-dependent rendering of large isosurfaces
Proceedings of the conference on Visualization '02
Simplification of Tetrahedral Meshes with Error Bounds
IEEE Transactions on Visualization and Computer Graphics
Dynamic maintenance and visualization of molecular surfaces
Discrete Applied Mathematics - Special issue: Computational molecular biology series issue IV
Constant-Time Neighbor Finding in Hierarchical Tetrahedral Meshes
SMI '01 Proceedings of the International Conference on Shape Modeling & Applications
The asymptotic decider: resolving the ambiguity in marching cubes
VIS '91 Proceedings of the 2nd conference on Visualization '91
Selective Refinement Queries for Volume Visualization of Unstructured Tetrahedral Meshes
IEEE Transactions on Visualization and Computer Graphics
Interactive Protein Manipulation
Proceedings of the 14th IEEE Visualization 2003 (VIS'03)
Hi-index | 0.00 |
Electrostatic interactions play a central role in biological processes. Development of fast computational methods to solve the underlying Poisson-Boltzmann equation (PBE) is vital for biomolecular modeling and simulation package. In this paper, we propose new methods for efficiently computing the electrostatic potentials for large molecules by using the geometry of the molecular shapes to guide the computation. The accuracy and stability of the solution to the PBE is quite sensitive to the boundary layer between the solvent and the solute which defines the molecular surface. In this paper, we present a new interface-layer-focused PBE solver. First, we analytically construct the molecular surface of the molecule and compute a distance field from the surface. We then construct nested iso-surface layers outwards and inwards from the surface using the distance field. We have developed a volume simplification algorithm to adaptively adjust the density of the irregular grid based on the importance to the PBE solution. We have generalized the finite difference methods using Taylor series expansion on the irregular grids. Our algorithm achieves about three times speedup in the iterative solution process of PBE, with more accurate results on an analytical solvable testing case, compared with the popular optimized DelPhi program.