Title :
Computing smooth molecular surfaces
Author :
Varshney, Amitabh ; Brooks, Frederick P., Jr. ; Wright, William V.
Author_Institution :
North Carolina Univ., Chapel Hill, NC, USA
Abstract :
We consider how we set out to formulate a parallel analytical molecular surface algorithm that has expected linear complexity with respect to the total number of atoms in a molecule. To achieve this goal, we avoided computing the complete 3D regular triangulation over the entire set of atoms, a process that takes time O(n log n), where n is the number of atoms in the molecule. We aim to compute and display these surfaces at interactive rates, by taking advantage of advances in computational geometry, making further algorithmic improvements and parallelizing the computations.<>
Keywords :
computational complexity; computational geometry; parallel algorithms; physics computing; 3D regular triangulation; algorithmic improvements; computation time; computational geometry; interactive rates; linear complexity; parallel analytical molecular surface algorithm; smooth molecular surface computing; surface atoms; three dimensional triangulation; Algorithm design and analysis; Atomic measurements; Computational geometry; Computer displays; Concurrent computing; Performance analysis; Probes; Proteins; Solvents; Visualization;
Journal_Title :
Computer Graphics and Applications, IEEE
