Dynamic Maintenance and Visualization of Molecular Surfaces

Molecular surface computations are basic molecular modeling operations that are necessary to deal with in order to perform synthetic drug design. Computing and updating exact boundary representations of such molecular surfaces are critical steps that introduce for molecules the same geometric data structure used in the solid modeling community. This allows us to gain immediate access to a wide range of modeling operations/techniques that allow us to use a general solid modeling system as a molecular modeling interface: one could for example replace single atoms or entire protein bases. In this paper, we introduce efficient techniques for computing NURBS (non-uniform rational B-splines) boundary representations of molecular surfaces, providing also the option of trading accuracy of the representation for the efficiency of the computation, especially in a dynamic setting. In particular, we discuss two main classes of updates: one that keeps the topology of the molecular configuration fixed, and the more complicated case where the topology may be updated continuously. In general, the output generated is in a representation format that can be loaded into a standard solid modeling system. It can also be directly triangulated or rendered, possibly at different levels of resolution by a standard graphics library such as OpenGL without any additional effort.