CVC Seminar: Wed Jan 26 1:30-3pm ACES 4.304

Qin Zhang

Molecular Surfaces: Area, Volume, and Atomic Derivatives

We will survey several models and algorithms for computing molecular surfaces, the area and volume of these surfaces, and the derivatives of the area and volume with respect to the molecule’s atomic centers. This problem is important in many fields, especially in the implicit solvation model which is widely used in molecular dynamics, protein interactions, docking, fitting, etc. First, we summarize the known results focusing on the Gaussian molecular model and alpha shape theory. Later we question whether it is possible to use only one molecular surface model for all our computations, i.e., surface, area, volume and their derivatives. Related nonpolarized energy (force) calculations used in softwares such as Amber and Gromacs will be reviewed. The challenges before us and some heuristic ideas are provided for discussion.